Variant report

Variant	rs12539481
Chromosome Location	chr7:124534446-124534447
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:124522245..124524955-chr7:124533723..124536178,2	K562	blood:
2	chr7:124534351..124537236-chr7:124567413..124569702,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10230948	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10234698	0.87[ASN][1000 genomes]
rs10241745	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10256073	0.83[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs10266152	0.82[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs10268290	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10280030	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1031952	0.83[CEU][hapmap];0.88[CHB][hapmap]
rs1034794	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1034795	0.85[ASN][1000 genomes]
rs10954061	0.82[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs11761435	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs11766412	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11767519	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770818	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11771004	0.83[CEU][hapmap]
rs11772420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11972411	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978268	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12532038	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12533661	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534967	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12534983	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538061	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12706625	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13222197	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13228358	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1404897	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs1471570	0.83[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1541417	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1552116	0.80[CHB][hapmap]
rs1552117	0.80[CHB][hapmap]
rs17147465	0.87[ASN][1000 genomes]
rs17147723	0.82[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17147889	0.87[CHB][hapmap]
rs2101100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2127968	0.85[EUR][1000 genomes]
rs2127969	0.84[EUR][1000 genomes]
rs2127970	0.85[EUR][1000 genomes]
rs2291207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2299904	0.93[CHB][hapmap]
rs2402754	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2402761	0.83[EUR][1000 genomes]
rs28820412	0.84[EUR][1000 genomes]
rs2929322	0.87[CHB][hapmap]
rs33964002	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34326887	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35146319	0.88[EUR][1000 genomes]
rs35423300	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35550222	0.84[ASN][1000 genomes]
rs4141073	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4141075	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs4360236	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4501522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4639456	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs4728005	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs4728007	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4731210	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60678110	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62480260	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62480274	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6466951	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6466959	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663056	0.80[CHB][hapmap]
rs6943703	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6943797	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6945563	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946962	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963885	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6965957	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs6968018	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs716991	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7782296	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7782351	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7784168	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7784285	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7786989	0.84[EUR][1000 genomes]
rs7787570	0.83[EUR][1000 genomes]
rs7787804	0.95[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7794637	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7795610	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7796751	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7801755	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804052	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806890	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811124	0.80[CEU][hapmap]
rs9656320	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs967297	0.82[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]

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	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	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
6	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
7	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
8	esv1829082	chr7:124503189-124556473	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv889137	chr7:124513770-124584834	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv889138	chr7:124518766-124584834	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	esv2756137	chr7:124521049-124558049	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124462200-124568200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr7:124466400-124540800	Weak transcription	Right Ventricle	heart
3	chr7:124466400-124562200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr7:124466600-124563400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr7:124466800-124540800	Weak transcription	Gastric	stomach
6	chr7:124484200-124554400	Weak transcription	HUVEC	blood vessel
7	chr7:124487200-124534800	Weak transcription	Fetal Heart	heart
8	chr7:124490800-124540600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:124498200-124568800	Weak transcription	Brain Anterior Caudate	brain
10	chr7:124506600-124540600	Weak transcription	Aorta	Aorta
11	chr7:124506800-124540600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr7:124518000-124535200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr7:124520400-124534600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr7:124520400-124534800	Weak transcription	Brain Substantia Nigra	brain
15	chr7:124522800-124568400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr7:124525600-124535200	Weak transcription	Psoas Muscle	Psoas
17	chr7:124527200-124537400	Weak transcription	HMEC	breast
18	chr7:124527600-124562200	Weak transcription	A549	lung
19	chr7:124527600-124569000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:124527600-124569000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr7:124527800-124540400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr7:124527800-124540800	Weak transcription	Placenta	Placenta
23	chr7:124528000-124567400	Weak transcription	HepG2	liver
24	chr7:124528400-124542800	Weak transcription	Spleen	Spleen
25	chr7:124528600-124538800	Weak transcription	Brain Germinal Matrix	brain
26	chr7:124528800-124540400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:124529200-124542800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr7:124529800-124553400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr7:124529800-124564400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr7:124530000-124540800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:124530000-124569000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr7:124530200-124540600	Weak transcription	Fetal Muscle Leg	muscle
33	chr7:124530400-124540600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr7:124531000-124542600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:124531200-124540600	Weak transcription	Left Ventricle	heart
36	chr7:124531400-124540600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr7:124531400-124540600	Weak transcription	Fetal Intestine Large	intestine
38	chr7:124531400-124540800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr7:124531400-124559800	Weak transcription	Ovary	ovary
40	chr7:124531600-124540800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr7:124531800-124540600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr7:124532000-124540600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr7:124532000-124569000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr7:124532200-124540600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr7:124532200-124540800	Weak transcription	Adipose Nuclei	Adipose
46	chr7:124532400-124535200	Weak transcription	Primary T cells from cord blood	blood
47	chr7:124532400-124535400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr7:124532400-124535600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr7:124532400-124536000	Weak transcription	NH-A	brain
50	chr7:124532400-124537000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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