Variant report

Variant	rs3758196
Chromosome Location	chr9:3397937-3397938
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr9:3397817-3398023	GM12878	blood:	n/a	n/a
2	ZNF384	chr9:3397913-3398995	GM12878	blood:	n/a	n/a
3	ATF2	chr9:3397833-3398676	GM12878	blood:	n/a	n/a
4	RUNX3	chr9:3397914-3398537	GM12878	blood:	n/a	n/a
5	SPI1	chr9:3397770-3398561	GM12891	blood:	n/a	chr9:3398309-3398316 chr9:3398307-3398320 chr9:3398301-3398314 chr9:3398307-3398320
6	SPI1	chr9:3397775-3398576	HL-60	blood:	n/a	chr9:3398309-3398316 chr9:3398307-3398320 chr9:3398301-3398314 chr9:3398307-3398320
7	BCLAF1	chr9:3397900-3398826	GM12878	blood:	n/a	n/a
8	SPI1	chr9:3397722-3398030	GM12891	blood:	n/a	n/a
9	CUX1	chr9:3397769-3398454	GM12878	blood:	n/a	n/a
10	RCOR1	chr9:3397605-3398744	GM12878	blood:	n/a	n/a
11	NFIC	chr9:3397829-3398860	GM12878	blood:	n/a	n/a
12	SPI1	chr9:3397666-3398752	HL-60	blood:	n/a	chr9:3398309-3398316 chr9:3398307-3398320 chr9:3398301-3398314 chr9:3398307-3398320
13	CREB1	chr9:3397924-3398879	GM12878	blood:	n/a	n/a
14	STAT3	chr9:3397766-3398640	GM12878	blood:	n/a	chr9:3398357-3398368
15	SPI1	chr9:3397686-3398708	GM12878	blood:	n/a	chr9:3398309-3398316 chr9:3398307-3398320 chr9:3398301-3398314 chr9:3398307-3398320
16	RUNX3	chr9:3397798-3398633	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RFX3	TF binding region

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10115757	0.92[CEU][hapmap];0.88[JPT][hapmap]
rs10115791	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs10117357	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs10117431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10117846	0.92[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap]
rs10124292	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10124295	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs10511447	0.89[CHB][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap]
rs10814019	0.82[ASN][1000 genomes]
rs10814096	0.89[JPT][hapmap]
rs10814097	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10971599	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs10971665	0.89[CHB][hapmap]
rs10971667	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs10971806	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10972042	0.89[JPT][hapmap]
rs10972079	0.84[CEU][hapmap]
rs11536748	0.82[EUR][1000 genomes]
rs12002215	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12115798	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs12337095	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs12338587	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12338927	0.82[EUR][1000 genomes]
rs12339955	0.88[JPT][hapmap]
rs12340535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12341652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12341737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12343385	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12346432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347068	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs12347811	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12347985	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes]
rs12554323	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs13283163	0.89[CHB][hapmap]
rs13286511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13290412	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13295925	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs13297034	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs13298219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13298908	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13300358	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs13301035	0.80[ASN][1000 genomes]
rs13302664	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13302841	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs16917371	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs16924266	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs1998976	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34065256	0.92[EUR][1000 genomes]
rs34086781	0.81[EUR][1000 genomes]
rs34123151	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34233417	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34283600	0.83[ASN][1000 genomes]
rs34331766	0.92[EUR][1000 genomes]
rs34708788	0.82[EUR][1000 genomes]
rs34774267	0.84[ASN][1000 genomes]
rs35079722	0.83[ASN][1000 genomes]
rs35412653	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35545940	0.82[EUR][1000 genomes]
rs35625648	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35824006	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35945655	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3758195	1.00[CEU][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes]
rs4741825	1.00[CEU][hapmap]
rs4741826	0.85[EUR][1000 genomes]
rs4741829	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4741834	0.86[CHD][hapmap]
rs60796901	0.92[EUR][1000 genomes]
rs6476436	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs6476451	0.80[EUR][1000 genomes]
rs66463406	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66763574	0.82[EUR][1000 genomes]
rs7021584	0.89[CHB][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap]
rs7022682	0.89[CHB][hapmap]
rs7026530	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs7028812	0.92[CEU][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7029544	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs7040113	0.92[CEU][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs7041836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7043493	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7045360	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs71506638	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71506639	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71506645	0.82[EUR][1000 genomes]
rs768485	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs7853728	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs7854273	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs7864440	0.89[JPT][hapmap]
rs7864459	0.89[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap]
rs9298952	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs9695619	1.00[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv613147	chr9:3368111-3440355	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv1849738	chr9:3389223-3404434	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
12	nsv892090	chr9:3391364-3496660	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3351000-3408200	Weak transcription	Fetal Intestine Small	intestine
2	chr9:3369400-3398400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr9:3377600-3401400	Weak transcription	HMEC	breast
4	chr9:3377800-3401600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:3382200-3425000	Weak transcription	Aorta	Aorta
6	chr9:3382400-3401400	Weak transcription	Brain Anterior Caudate	brain
7	chr9:3382800-3401000	Weak transcription	Brain Germinal Matrix	brain
8	chr9:3383200-3410000	Weak transcription	Fetal Brain Male	brain
9	chr9:3383400-3401400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:3386000-3398000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr9:3386200-3409600	Weak transcription	Psoas Muscle	Psoas
12	chr9:3387200-3401000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr9:3387200-3433800	Weak transcription	Pancreas	Pancrea
14	chr9:3387800-3401400	Weak transcription	Brain Hippocampus Middle	brain
15	chr9:3388000-3401400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:3388200-3401400	Weak transcription	Brain Substantia Nigra	brain
17	chr9:3388600-3401800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:3388800-3401800	Weak transcription	Fetal Stomach	stomach
19	chr9:3389200-3398600	Weak transcription	Spleen	Spleen
20	chr9:3390600-3398600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr9:3390600-3398600	Weak transcription	Thymus	Thymus
22	chr9:3390800-3398400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:3390800-3401200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:3390800-3401600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:3391000-3401800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:3391800-3401200	Weak transcription	Brain Angular Gyrus	brain
27	chr9:3392200-3398800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:3392400-3401200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:3393600-3401400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr9:3395000-3398200	Weak transcription	HSMM	muscle
31	chr9:3395000-3401000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr9:3395400-3398400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr9:3395600-3398000	Weak transcription	Adipose Nuclei	Adipose
34	chr9:3395600-3398400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr9:3395600-3400800	Weak transcription	Fetal Brain Female	brain
36	chr9:3395800-3401400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:3396000-3401000	Weak transcription	Fetal Lung	lung
38	chr9:3396800-3398000	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr9:3396800-3398200	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr9:3396800-3398200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr9:3396800-3398400	Weak transcription	Small Intestine	intestine
42	chr9:3396800-3398400	Enhancers	Dnd41	blood
43	chr9:3396800-3401400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:3397000-3398000	Enhancers	Primary hematopoietic stem cells	blood
45	chr9:3397000-3398200	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr9:3397000-3398600	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr9:3397000-3398800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr9:3397200-3398600	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr9:3397400-3398200	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr9:3397400-3398200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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