Variant report

Variant	rs12532038
Chromosome Location	chr7:124494465-124494466
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:124482329..124484831-chr7:124493791..124496248,2	K562	blood:
2	chr7:124481779..124483829-chr7:124493463..124496248,2	K562	blood:

Variant related genes	Relation type
ENSG00000128513	Chromatin interaction

Extended variants
information (count: 130 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10156168	0.82[ASW][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs10228376	0.82[ASW][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs10228682	0.82[ASW][hapmap];0.92[YRI][hapmap]
rs10230948	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10234698	0.90[ASN][1000 genomes]
rs10241745	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10250911	0.82[ASW][hapmap];0.92[YRI][hapmap]
rs10256073	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs10263573	0.92[YRI][hapmap]
rs10266152	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap]
rs10268290	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10271687	0.81[AFR][1000 genomes]
rs10272583	0.82[ASW][hapmap];0.87[YRI][hapmap]
rs10280030	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1034794	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1034795	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10954045	0.80[AFR][1000 genomes]
rs10954048	0.92[YRI][hapmap]
rs10954061	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap]
rs11761435	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap]
rs11766412	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11767519	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11768553	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11770818	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11772420	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11972411	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11975788	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs11980925	0.92[YRI][hapmap]
rs12154816	0.91[YRI][hapmap]
rs12155120	0.92[YRI][hapmap]
rs12530981	0.91[YRI][hapmap]
rs12533661	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12534967	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12534983	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12536575	0.92[YRI][hapmap]
rs12537983	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12538061	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12538333	0.82[ASW][hapmap];0.87[YRI][hapmap]
rs12539481	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12666427	0.82[ASW][hapmap];0.83[YRI][hapmap]
rs12706625	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12706627	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13222197	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13228358	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1404897	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap]
rs1471570	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs1481341	0.82[ASW][hapmap];0.92[YRI][hapmap]
rs1541417	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17147465	0.90[ASN][1000 genomes]
rs17147723	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap]
rs1904975	0.82[ASW][hapmap];0.92[YRI][hapmap]
rs2101100	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2286174	0.92[YRI][hapmap]
rs2291207	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2299904	0.93[CHB][hapmap]
rs2402754	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28730874	0.85[ASN][1000 genomes]
rs2896361	0.92[YRI][hapmap]
rs3213667	0.92[YRI][hapmap]
rs33964002	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34326887	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34600520	0.81[AFR][1000 genomes]
rs35423300	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35550222	0.88[ASN][1000 genomes]
rs3815221	0.82[ASW][hapmap];0.91[YRI][hapmap]
rs4141073	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4141075	0.93[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs4283967	0.82[ASW][hapmap]
rs4311608	0.91[YRI][hapmap]
rs4360236	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4377885	0.82[ASW][hapmap];0.92[YRI][hapmap]
rs4463363	0.82[ASW][hapmap];0.92[YRI][hapmap]
rs4501522	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4639456	0.93[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs4728005	0.93[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs4728007	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4728009	0.82[ASW][hapmap];0.91[YRI][hapmap]
rs4728011	0.91[YRI][hapmap]
rs4731210	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4731216	0.92[YRI][hapmap]
rs4731218	0.81[ASW][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap]
rs60678110	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62480260	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62480274	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6466951	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6466952	0.80[AFR][1000 genomes]
rs6466959	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6943703	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6943797	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6945104	0.82[ASW][hapmap];0.88[YRI][hapmap]
rs6945563	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6946962	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6953168	0.81[AFR][1000 genomes]
rs6963885	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6965957	0.86[CHB][hapmap]
rs6968018	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6973812	0.82[ASW][hapmap];0.92[YRI][hapmap]
rs716991	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs727506	0.92[YRI][hapmap]
rs7357296	0.92[YRI][hapmap]
rs7778544	0.92[YRI][hapmap]
rs7782031	0.81[AFR][1000 genomes]
rs7782296	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7782327	0.81[AFR][1000 genomes]
rs7782340	0.80[AFR][1000 genomes]
rs7782351	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7784168	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7784285	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7787804	0.91[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7789859	0.87[YRI][hapmap]
rs7794637	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7795492	0.82[ASW][hapmap];0.92[YRI][hapmap]
rs7795610	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7796751	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7799938	0.92[YRI][hapmap]
rs7801140	0.80[AFR][1000 genomes]
rs7801755	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7804052	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7806890	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9656320	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs967297	0.87[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap]
rs9886177	0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429809	chr7:123937674-124835925	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	esv3446198	chr7:124358002-124586856	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv889134	chr7:124462081-124552802	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv889135	chr7:124462081-124584834	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv1792357	chr7:124470044-124506088	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv464707	chr7:124486980-124572288	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv608341	chr7:124486980-124572288	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv889136	chr7:124492038-124552802	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12532038	IMPDH1	cis	cerebellum	SCAN
rs12532038	WASL	cis	cerebellum	SCAN
rs12532038	IMPDH1	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124454400-124497600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:124454600-124501400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:124457600-124497600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr7:124459000-124497800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:124459200-124497600	Weak transcription	Pancreas	Pancrea
6	chr7:124459200-124499400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:124459400-124497600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:124459400-124497600	Weak transcription	Brain Anterior Caudate	brain
9	chr7:124461000-124499200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:124461000-124499600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr7:124461400-124530800	Weak transcription	NHDF-Ad	bronchial
12	chr7:124461600-124499800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr7:124462200-124495000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:124462200-124498200	Weak transcription	Psoas Muscle	Psoas
15	chr7:124462200-124510200	Weak transcription	Brain Angular Gyrus	brain
16	chr7:124462200-124568200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr7:124462400-124497400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:124462600-124504000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr7:124464000-124506400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:124464000-124510400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr7:124464200-124519400	Weak transcription	Brain Hippocampus Middle	brain
22	chr7:124464400-124497200	Weak transcription	Brain Germinal Matrix	brain
23	chr7:124464400-124497600	Weak transcription	Lung	lung
24	chr7:124464400-124508800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr7:124464600-124530600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:124466400-124497600	Weak transcription	Fetal Thymus	thymus
27	chr7:124466400-124497600	Weak transcription	Spleen	Spleen
28	chr7:124466400-124540800	Weak transcription	Right Ventricle	heart
29	chr7:124466400-124562200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr7:124466600-124563400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr7:124466800-124497600	Weak transcription	Aorta	Aorta
32	chr7:124466800-124497800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr7:124466800-124540800	Weak transcription	Gastric	stomach
34	chr7:124467000-124497400	Weak transcription	Ovary	ovary
35	chr7:124467000-124508200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr7:124467400-124497400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:124467600-124530600	Weak transcription	NH-A	brain
38	chr7:124467800-124510600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr7:124474200-124509600	Weak transcription	HMEC	breast
40	chr7:124475400-124497400	Weak transcription	Thymus	Thymus
41	chr7:124475400-124497600	Weak transcription	Left Ventricle	heart
42	chr7:124475400-124506000	Weak transcription	Fetal Kidney	kidney
43	chr7:124475400-124506000	Weak transcription	Fetal Lung	lung
44	chr7:124475400-124511400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:124477000-124530800	Weak transcription	Primary B cells from peripheral blood	blood
46	chr7:124480600-124497600	Weak transcription	Fetal Intestine Large	intestine
47	chr7:124482200-124497400	Weak transcription	Fetal Brain Female	brain
48	chr7:124482400-124508200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr7:124482400-124508600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr7:124483400-124497000	Weak transcription	A549	lung

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