Variant report

Variant	rs10254829
Chromosome Location	chr7:150213151-150213152
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	POLR2A	chr7:150212879-150213927	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr7:150211611-150213235	GM12891	blood:	n/a	n/a
3	POLR2A	chr7:150211428-150213403	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
STRADBP1	TF binding region

Extended variants
information (count: 156 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10952277	0.81[EUR][1000 genomes]
rs11486916	0.86[EUR][1000 genomes]
rs11761189	0.86[EUR][1000 genomes]
rs11764032	0.83[EUR][1000 genomes]
rs11764049	0.83[EUR][1000 genomes]
rs11764138	0.83[EUR][1000 genomes]
rs11764186	0.86[EUR][1000 genomes]
rs11764483	0.86[EUR][1000 genomes]
rs11766379	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11767574	0.82[EUR][1000 genomes]
rs11767598	0.84[EUR][1000 genomes]
rs11769703	0.91[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs11769828	0.90[EUR][1000 genomes]
rs11770334	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11771827	0.90[EUR][1000 genomes]
rs11981436	0.86[EUR][1000 genomes]
rs11981515	0.86[EUR][1000 genomes]
rs11981976	0.83[EUR][1000 genomes]
rs11982037	0.83[EUR][1000 genomes]
rs12154687	0.82[EUR][1000 genomes]
rs1234357	0.82[JPT][hapmap]
rs12397707	0.80[EUR][1000 genomes]
rs12530578	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532846	0.88[EUR][1000 genomes]
rs12533735	0.90[EUR][1000 genomes]
rs12535647	0.90[EUR][1000 genomes]
rs12537789	0.85[CEU][hapmap]
rs12666582	0.82[EUR][1000 genomes]
rs12671272	0.86[EUR][1000 genomes]
rs12671275	0.86[EUR][1000 genomes]
rs12673131	0.85[EUR][1000 genomes]
rs12673133	0.86[EUR][1000 genomes]
rs12673168	0.86[EUR][1000 genomes]
rs12673197	0.84[EUR][1000 genomes]
rs13220967	0.82[EUR][1000 genomes]
rs13221085	0.80[EUR][1000 genomes]
rs13222892	0.87[EUR][1000 genomes]
rs13223299	0.83[EUR][1000 genomes]
rs13223343	0.80[EUR][1000 genomes]
rs13223653	0.81[EUR][1000 genomes]
rs13225097	0.82[EUR][1000 genomes]
rs13225393	0.82[EUR][1000 genomes]
rs13225610	0.82[EUR][1000 genomes]
rs13226396	0.82[EUR][1000 genomes]
rs13232683	0.86[EUR][1000 genomes]
rs13232785	0.83[EUR][1000 genomes]
rs13232989	0.86[EUR][1000 genomes]
rs13234724	0.81[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs13235529	0.86[EUR][1000 genomes]
rs13235632	0.85[EUR][1000 genomes]
rs13235707	0.90[EUR][1000 genomes]
rs13236567	0.86[EUR][1000 genomes]
rs13236678	0.82[EUR][1000 genomes]
rs13240099	0.82[EUR][1000 genomes]
rs13240106	0.82[EUR][1000 genomes]
rs1578916	0.86[EUR][1000 genomes]
rs1608158	0.90[EUR][1000 genomes]
rs17837503	0.80[EUR][1000 genomes]
rs2204131	0.87[EUR][1000 genomes]
rs2373805	0.86[EUR][1000 genomes]
rs2373806	0.86[EUR][1000 genomes]
rs2888664	0.86[EUR][1000 genomes]
rs34035483	0.86[EUR][1000 genomes]
rs34079857	0.86[EUR][1000 genomes]
rs34097488	0.86[EUR][1000 genomes]
rs34118164	0.86[EUR][1000 genomes]
rs34176120	0.86[EUR][1000 genomes]
rs34476103	0.86[EUR][1000 genomes]
rs34534990	0.86[EUR][1000 genomes]
rs34803745	0.86[EUR][1000 genomes]
rs34815266	0.80[EUR][1000 genomes]
rs34822032	0.90[EUR][1000 genomes]
rs34900736	0.81[EUR][1000 genomes]
rs35113886	0.85[EUR][1000 genomes]
rs35114152	0.83[EUR][1000 genomes]
rs35182796	0.82[EUR][1000 genomes]
rs35188092	0.86[EUR][1000 genomes]
rs35222868	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35233281	0.86[EUR][1000 genomes]
rs35241484	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35276692	0.84[EUR][1000 genomes]
rs35346811	0.86[EUR][1000 genomes]
rs35428045	0.86[EUR][1000 genomes]
rs35432864	0.82[EUR][1000 genomes]
rs35464700	0.80[EUR][1000 genomes]
rs35492812	0.80[EUR][1000 genomes]
rs35512856	0.83[EUR][1000 genomes]
rs35659213	0.86[EUR][1000 genomes]
rs35737876	0.83[EUR][1000 genomes]
rs35821632	0.85[EUR][1000 genomes]
rs35873531	0.83[EUR][1000 genomes]
rs36200127	0.86[EUR][1000 genomes]
rs3735080	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735086	0.82[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs3807382	0.91[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs4339549	0.86[EUR][1000 genomes]
rs4339550	0.83[EUR][1000 genomes]
rs4367453	0.82[EUR][1000 genomes]
rs4382385	0.83[EUR][1000 genomes]
rs4543461	0.86[EUR][1000 genomes]
rs4573169	0.86[EUR][1000 genomes]
rs4584065	0.86[EUR][1000 genomes]
rs57729315	0.86[EUR][1000 genomes]
rs57899656	0.85[EUR][1000 genomes]
rs58391005	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60213500	0.84[EUR][1000 genomes]
rs62502277	0.86[EUR][1000 genomes]
rs62502293	0.86[EUR][1000 genomes]
rs62502294	0.84[EUR][1000 genomes]
rs62502295	0.85[EUR][1000 genomes]
rs62502296	0.83[EUR][1000 genomes]
rs62502297	0.83[EUR][1000 genomes]
rs62502298	0.86[EUR][1000 genomes]
rs62502300	0.86[EUR][1000 genomes]
rs62502326	0.86[EUR][1000 genomes]
rs62503201	0.87[EUR][1000 genomes]
rs62504164	0.80[EUR][1000 genomes]
rs62504165	0.82[EUR][1000 genomes]
rs6942848	0.86[EUR][1000 genomes]
rs6950079	0.86[EUR][1000 genomes]
rs6950421	0.86[EUR][1000 genomes]
rs6951360	0.86[EUR][1000 genomes]
rs6954076	0.82[EUR][1000 genomes]
rs6954709	0.86[EUR][1000 genomes]
rs6954884	0.86[EUR][1000 genomes]
rs6954937	0.86[EUR][1000 genomes]
rs6969250	0.83[EUR][1000 genomes]
rs6971133	0.81[EUR][1000 genomes]
rs6971221	0.82[EUR][1000 genomes]
rs6971529	0.82[EUR][1000 genomes]
rs6978270	0.86[EUR][1000 genomes]
rs6978778	0.86[EUR][1000 genomes]
rs71539836	0.86[EUR][1000 genomes]
rs73161782	0.90[EUR][1000 genomes]
rs73163513	0.83[EUR][1000 genomes]
rs7455366	0.90[EUR][1000 genomes]
rs7781524	0.86[EUR][1000 genomes]
rs7781992	0.86[EUR][1000 genomes]
rs7783326	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784108	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7788112	0.82[EUR][1000 genomes]
rs7788300	0.82[EUR][1000 genomes]
rs7788683	0.82[EUR][1000 genomes]
rs7788885	0.82[EUR][1000 genomes]
rs7796338	0.86[EUR][1000 genomes]
rs7808446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9768447	0.82[EUR][1000 genomes]

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	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv1025129	chr7:150146593-150266217	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1031309	chr7:150171651-150222230	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3395746	chr7:150181141-150300680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10254829	FLJ37035	trans	parietal	SCAN
rs10254829	GIMAP4	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150211000-150213200	Active TSS	Lung	lung
2	chr7:150211000-150214600	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr7:150211000-150214800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
4	chr7:150211000-150216200	Active TSS	Psoas Muscle	Psoas
5	chr7:150211000-150219000	Active TSS	Right Atrium	heart
6	chr7:150211200-150214800	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr7:150211200-150217000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr7:150211400-150214600	Active TSS	Brain Anterior Caudate	brain
9	chr7:150211400-150215400	Active TSS	Left Ventricle	heart
10	chr7:150211400-150217400	Active TSS	Adipose Nuclei	Adipose
11	chr7:150211400-150218600	Active TSS	Duodenum Mucosa	Duodenum
12	chr7:150211600-150213200	Active TSS	Brain Cingulate Gyrus	brain
13	chr7:150211600-150213200	Active TSS	Brain Substantia Nigra	brain
14	chr7:150211600-150213200	Active TSS	Esophagus	oesophagus
15	chr7:150211600-150213400	Active TSS	Fetal Intestine Small	intestine
16	chr7:150211600-150214200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr7:150211600-150214200	Active TSS	Fetal Intestine Large	intestine
18	chr7:150211600-150214600	Active TSS	Stomach Smooth Muscle	stomach
19	chr7:150211600-150214800	Active TSS	Liver	Liver
20	chr7:150211600-150215400	Active TSS	Rectal Smooth Muscle	rectum
21	chr7:150211600-150215400	Active TSS	Right Ventricle	heart
22	chr7:150211600-150215400	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr7:150211600-150215800	Active TSS	Monocytes-CD14+_RO01746	blood
24	chr7:150211600-150216000	Active TSS	Fetal Muscle Leg	muscle
25	chr7:150211600-150216800	Active TSS	Primary monocytes fromperipheralblood	blood
26	chr7:150211600-150216800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr7:150211600-150217000	Active TSS	Primary T cells from cord blood	blood
28	chr7:150211600-150217000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr7:150211800-150213200	Active TSS	Fetal Muscle Trunk	muscle
30	chr7:150211800-150213600	Active TSS	Fetal Stomach	stomach
31	chr7:150211800-150214200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr7:150211800-150214800	Active TSS	Fetal Kidney	kidney
33	chr7:150211800-150215400	Active TSS	Thymus	Thymus
34	chr7:150211800-150216200	Active TSS	GM12878-XiMat	blood
35	chr7:150211800-150216800	Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr7:150211800-150216800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr7:150211800-150216800	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr7:150211800-150217000	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr7:150212000-150213200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
40	chr7:150212000-150213200	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr7:150212000-150213200	Active TSS	Gastric	stomach
42	chr7:150212000-150213200	Active TSS	Pancreas	Pancrea
43	chr7:150212000-150213200	Active TSS	Spleen	Spleen
44	chr7:150212000-150213400	Active TSS	Dnd41	blood
45	chr7:150212000-150214000	Active TSS	Placenta	Placenta
46	chr7:150212000-150215400	Active TSS	Small Intestine	intestine
47	chr7:150212200-150213600	Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr7:150212200-150213800	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr7:150212200-150213800	Active TSS	HUVEC	blood vessel
50	chr7:150212200-150216200	Active TSS	Fetal Thymus	thymus

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