Variant report

Variant	rs7586229
Chromosome Location	chr2:95945830-95945831
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10195614	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1104775	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164122	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs11897976	0.90[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs12992066	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1559483	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs17119148	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs1862897	0.90[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs1875402	1.00[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs1966272	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2001254	0.83[EUR][1000 genomes]
rs2010533	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2042477	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs2098768	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2113417	0.90[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs2320339	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2320621	0.83[EUR][1000 genomes]
rs2320624	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3105102	0.81[EUR][1000 genomes]
rs3105104	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes]
rs3105105	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112221	0.84[EUR][1000 genomes]
rs3112223	0.84[EUR][1000 genomes]
rs3112225	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs3112228	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3112229	0.97[CHD][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs3112230	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112995	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs3112996	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs3112997	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs3112999	0.81[EUR][1000 genomes]
rs3113000	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3113001	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3755519	0.88[EUR][1000 genomes]
rs3755520	0.86[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs3755521	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs3755523	0.86[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs3755525	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs3772031	0.90[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs3772032	0.90[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs3772033	0.90[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs3772034	0.83[EUR][1000 genomes]
rs3772037	0.88[EUR][1000 genomes]
rs3772041	0.86[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs3772042	0.86[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs3772043	0.86[CEU][hapmap];0.91[EUR][1000 genomes]
rs3772044	0.95[CEU][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs3821341	0.81[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs4283455	0.88[EUR][1000 genomes]
rs4854247	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4854249	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6577012	0.86[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs6577013	0.86[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs6715813	0.86[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs6719098	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6725821	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6741001	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs6750542	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs7574862	0.86[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs7580685	0.86[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs7585914	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594144	0.88[CEU][hapmap];0.83[JPT][hapmap];0.89[EUR][1000 genomes]
rs7602807	0.87[EUR][1000 genomes]
rs870393	0.81[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs889851	0.86[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs889852	0.86[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs889853	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs918811	0.90[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs9678800	0.90[CEU][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs9989786	0.81[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv817299	chr2:95799814-96159275	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1007627	chr2:95878031-95973743	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv535822	chr2:95878031-95973743	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv998370	chr2:95897299-96074071	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv535823	chr2:95897299-96074071	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv998014	chr2:95913278-96296630	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv528011	chr2:95931218-96057011	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1003196	chr2:95935031-95988314	Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1010831	chr2:95935648-96074213	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv535824	chr2:95935648-96074213	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv482871	chr2:95936531-96036880	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv1010345	chr2:95939355-95988314	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7586229	KCNIP3	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95925600-95953800	Weak transcription	Right Atrium	heart
2	chr2:95926800-95953600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:95930000-95956200	Weak transcription	Fetal Brain Female	brain
4	chr2:95931400-95961000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:95931400-95961600	Weak transcription	Brain Substantia Nigra	brain
6	chr2:95932400-95961600	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:95938200-95947800	Weak transcription	Brain Germinal Matrix	brain
8	chr2:95941800-95954600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:95942800-95947000	Genic enhancers	Esophagus	oesophagus
10	chr2:95943000-95951400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:95943400-95952600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:95943600-95952600	Weak transcription	Lung	lung
13	chr2:95943600-95956200	Weak transcription	Right Ventricle	heart
14	chr2:95943800-95949000	Weak transcription	Fetal Intestine Small	intestine
15	chr2:95943800-95950800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:95944000-95947400	Weak transcription	Placenta	Placenta
17	chr2:95944400-95947800	Weak transcription	Pancreas	Pancrea
18	chr2:95944600-95946000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:95944600-95947400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:95944600-95949600	Strong transcription	Gastric	stomach
21	chr2:95944600-95955000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:95944800-95946400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:95944800-95947800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:95944800-95948400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:95944800-95948600	Weak transcription	Spleen	Spleen
26	chr2:95944800-95949000	Strong transcription	HMEC	breast
27	chr2:95944800-95953600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:95944800-95955000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:95945200-95946600	Strong transcription	Colonic Mucosa	Colon
30	chr2:95945200-95947400	Weak transcription	Fetal Stomach	stomach
31	chr2:95945400-95946800	Strong transcription	Stomach Mucosa	stomach
32	chr2:95945400-95948600	Strong transcription	NHEK	skin
33	chr2:95945800-95946600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr2:95945800-95949400	Strong transcription	Duodenum Mucosa	Duodenum
35	chr2:95945800-95956400	Weak transcription	Ovary	ovary
36	chr2:95945800-95958200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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