Variant report

Variant	rs4077399
Chromosome Location	chr9:140849018-140849019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10732689	0.80[YRI][hapmap]
rs10735530	0.82[YRI][hapmap]
rs10780196	0.83[CEU][hapmap];0.95[TSI][hapmap]
rs10867090	0.81[LWK][hapmap];0.85[YRI][hapmap]
rs10867093	0.82[CEU][hapmap]
rs11137299	0.82[ASN][1000 genomes]
rs11137317	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11137332	0.80[EUR][1000 genomes]
rs11137335	0.83[CEU][hapmap];0.87[TSI][hapmap]
rs1123190	0.90[JPT][hapmap]
rs12005780	0.95[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap]
rs12352971	0.86[CHB][hapmap]
rs1547503	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1547504	0.81[JPT][hapmap]
rs2124655	0.83[CEU][hapmap];0.95[TSI][hapmap]
rs2168526	0.83[CEU][hapmap];0.95[TSI][hapmap]
rs28417558	0.81[AMR][1000 genomes]
rs41277867	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59194462	0.85[EUR][1000 genomes]
rs62589625	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62589636	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62589643	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6559255	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7023346	0.83[CEU][hapmap];1.00[TSI][hapmap]
rs7023369	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs7023861	0.81[AMR][1000 genomes]
rs7028989	0.83[CEU][hapmap];0.95[TSI][hapmap]
rs7032972	0.80[ASN][1000 genomes]
rs7034441	0.81[AMR][1000 genomes]
rs7034745	0.82[YRI][hapmap]
rs7035007	0.83[CEU][hapmap]
rs7035895	0.83[CEU][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs7035939	0.83[CEU][hapmap];0.95[TSI][hapmap]
rs7040050	0.83[CEU][hapmap];0.95[TSI][hapmap]
rs7042228	0.84[EUR][1000 genomes]
rs7043116	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7043700	0.83[CEU][hapmap];1.00[TSI][hapmap]
rs7045820	0.83[AMR][1000 genomes]
rs7046931	0.81[LWK][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes]
rs7047822	0.82[CEU][hapmap]
rs7847988	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs7850056	0.94[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7860115	0.84[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs7868607	0.82[CEU][hapmap];0.81[LWK][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes]
rs7869398	0.83[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes]
rs7869557	0.83[CEU][hapmap]
rs7869841	0.85[JPT][hapmap]
rs7870040	0.83[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs7870208	0.83[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs936248	0.83[CEU][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:40 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531654	chr9:140110329-141033187	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	281 gene(s)	inside rSNPs	diseases
2	nsv932633	chr9:140240417-141053535	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1053628	chr9:140260666-141005637	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
4	nsv534215	chr9:140286134-141008915	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	n/a
5	nsv531665	chr9:140378700-141073897	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	n/a
6	nsv868924	chr9:140407572-141053525	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	n/a
7	nsv1039933	chr9:140408112-141005637	Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	n/a
8	nsv531666	chr9:140409395-141015925	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	n/a
9	nsv1052036	chr9:140452641-141018985	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
10	nsv540365	chr9:140452641-141018985	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
11	nsv949702	chr9:140466816-141027939	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	n/a
12	nsv531667	chr9:140468821-140936261	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
13	nsv531668	chr9:140492807-140986221	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	n/a
14	nsv531669	chr9:140514663-140852911	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	n/a
15	nsv1053192	chr9:140532404-141005637	Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
16	nsv540366	chr9:140532404-141005637	Weak transcription Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
17	nsv1038090	chr9:140575692-141005637	Genic enhancers ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
18	nsv1042984	chr9:140581700-140854178	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	n/a
19	nsv1046076	chr9:140612799-140892404	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	n/a
20	nsv1055039	chr9:140612799-141005637	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	n/a
21	nsv540368	chr9:140612799-141005637	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	n/a
22	nsv1039470	chr9:140630889-141005637	ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	n/a
23	nsv894678	chr9:140632837-140924465	ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	n/a
24	nsv1044418	chr9:140686097-141005637	Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	n/a
25	nsv428228	chr9:140719304-141153431	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	n/a
26	nsv869452	chr9:140724997-141018984	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	n/a
27	nsv1038487	chr9:140746220-140875798	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
28	nsv1044352	chr9:140757062-141018985	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
29	nsv540371	chr9:140757062-141018985	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
30	nsv491650	chr9:140757063-140954147	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
31	nsv1046177	chr9:140796372-141019124	Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
32	nsv540372	chr9:140796372-141019124	Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
33	nsv917477	chr9:140796572-141073897	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
34	nsv894680	chr9:140801512-140978576	Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
35	nsv1046169	chr9:140801859-141018985	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
36	nsv540373	chr9:140801859-141018985	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
37	nsv1037624	chr9:140803971-141005637	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
38	nsv540374	chr9:140803971-141005637	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
39	nsv894681	chr9:140816423-140938183	Strong transcription Genic enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
40	nsv1040618	chr9:140817187-141005637	Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4077399	C8G	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:140843600-140849200	Weak transcription	Brain Angular Gyrus	brain
2	chr9:140843600-140855600	Weak transcription	Right Atrium	heart
3	chr9:140844000-140851200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:140844000-140854200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:140844000-140860600	Weak transcription	Fetal Brain Male	brain
6	chr9:140844400-140854600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:140845200-140866200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:140846200-140849800	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr9:140846200-140853000	Strong transcription	Brain Germinal Matrix	brain
10	chr9:140846800-140853200	Strong transcription	Fetal Brain Female	brain
11	chr9:140847000-140851400	Weak transcription	Spleen	Spleen
12	chr9:140847400-140864000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:140847600-140850800	Enhancers	Brain Anterior Caudate	brain
14	chr9:140848600-140850000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:140848800-140849800	Enhancers	Brain Substantia Nigra	brain
16	chr9:140848800-140851200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:140849000-140849200	Enhancers	Brain Hippocampus Middle	brain
18	chr9:140849000-140849400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:140849000-140850000	Enhancers	Brain Cingulate Gyrus	brain

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