Variant report

Variant	rs7029544
Chromosome Location	chr9:3360355-3360356
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10117357	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10117431	1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs10124292	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs10124295	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10511447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10814019	0.81[AMR][1000 genomes]
rs10814038	0.87[YRI][hapmap]
rs10814039	0.82[YRI][hapmap]
rs10814097	0.88[JPT][hapmap]
rs10971534	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10971535	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10971599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10971661	0.83[YRI][hapmap]
rs10971665	0.81[YRI][hapmap]
rs10971667	1.00[JPT][hapmap]
rs12002215	1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs12115798	0.88[JPT][hapmap]
rs12335763	0.82[YRI][hapmap]
rs12338746	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340535	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs12341652	0.89[JPT][hapmap]
rs12341737	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs12346432	0.89[JPT][hapmap]
rs12347068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12554323	0.88[JPT][hapmap]
rs13286511	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13290412	0.89[JPT][hapmap]
rs13298219	0.89[JPT][hapmap]
rs13300358	0.89[JPT][hapmap]
rs13302664	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13302841	0.88[JPT][hapmap]
rs1348369	0.86[YRI][hapmap]
rs16917371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16924266	0.89[JPT][hapmap]
rs1998976	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs2986682	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35945655	0.81[ASN][1000 genomes]
rs3758196	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs4237147	0.83[YRI][hapmap]
rs4741825	0.84[YRI][hapmap]
rs56829164	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66463406	0.83[ASN][1000 genomes]
rs7021584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7022682	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028812	0.88[JPT][hapmap]
rs7041836	0.89[JPT][hapmap]
rs7043493	1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7045360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs768485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7858850	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7860163	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7864459	0.88[JPT][hapmap]
rs7869854	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870914	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875889	0.87[YRI][hapmap]
rs9298952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv466091	chr9:3349487-3389660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv613146	chr9:3349487-3389660	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3288200-3378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:3337800-3388800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr9:3341200-3397600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr9:3350600-3360800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr9:3351000-3408200	Weak transcription	Fetal Intestine Small	intestine
6	chr9:3351400-3361400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:3354600-3364600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr9:3355000-3383800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr9:3355400-3365600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:3356400-3360400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr9:3359200-3361200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr9:3359200-3361200	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr9:3359200-3361400	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr9:3359200-3361400	Enhancers	Liver	Liver
15	chr9:3359400-3361000	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr9:3359400-3383200	Weak transcription	Primary T cells from cord blood	blood
17	chr9:3359400-3387600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr9:3359600-3360800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr9:3359600-3361400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr9:3359600-3369600	Weak transcription	Pancreas	Pancrea
21	chr9:3359600-3383800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:3359800-3362600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr9:3359800-3364000	Weak transcription	Left Ventricle	heart
24	chr9:3359800-3365800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:3359800-3384000	Weak transcription	Primary B cells from cord blood	blood
26	chr9:3360200-3361200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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