Variant report

Variant	rs10835508
Chromosome Location	chr11:4045360-4045361
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1013351	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10500590	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs10742200	0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs10767702	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10767713	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10767715	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10767767	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10767811	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10835311	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10835312	0.82[EUR][1000 genomes]
rs10835331	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10835337	0.83[YRI][hapmap]
rs10835340	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs10835359	0.87[EUR][1000 genomes]
rs10835399	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835402	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835403	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835406	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835407	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835454	0.87[EUR][1000 genomes]
rs10835474	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10835521	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835540	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10835545	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10835554	0.85[ASN][1000 genomes]
rs10835556	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10835557	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10835561	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835596	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835597	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835601	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835604	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835611	0.81[CHB][hapmap]
rs11030276	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11030404	0.84[YRI][hapmap]
rs11030579	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11030580	0.82[ASN][1000 genomes]
rs11030599	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11030627	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11030631	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11030639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11030660	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11030781	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11493482	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12223176	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12270732	0.81[YRI][hapmap]
rs12281293	0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes]
rs12283447	0.86[EUR][1000 genomes]
rs12286710	0.95[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes]
rs12290747	0.83[EUR][1000 genomes]
rs1349583	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1442726	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1452047	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1452048	0.85[YRI][hapmap]
rs17081	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17279635	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2119987	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412338	0.85[YRI][hapmap];0.81[EUR][1000 genomes]
rs28419002	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2898947	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs3817657	0.81[CHB][hapmap]
rs4910590	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4910596	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910597	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910598	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4910866	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4910868	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4910869	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4910875	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910877	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910880	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6578421	0.96[YRI][hapmap]
rs6578424	0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs66503725	0.87[EUR][1000 genomes]
rs66596383	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67065286	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67300156	0.85[EUR][1000 genomes]
rs7102215	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7113845	0.81[EUR][1000 genomes]
rs7128762	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7130580	0.81[CHB][hapmap]
rs714380	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs720571	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs723779	0.84[YRI][hapmap]
rs750525	0.84[YRI][hapmap]
rs7924984	0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs7932702	0.81[CHB][hapmap]
rs7935824	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950153	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs963998	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs995498	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS 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	21 gene(s)	inside rSNPs	diseases
4	nsv1042719	chr11:4017541-4101609	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10835508	STIM1	cis	lung	GTEx
rs10835508	RRM1	cis	Thyroid	GTEx
rs10835508	RRM1	cis	Artery Tibial	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4038000-4049400	Weak transcription	Spleen	Spleen
2	chr11:4038200-4048800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr11:4038200-4057200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:4038200-4065200	Weak transcription	Left Ventricle	heart
5	chr11:4038400-4045400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr11:4038400-4045400	Weak transcription	Psoas Muscle	Psoas
7	chr11:4038400-4065400	Weak transcription	Esophagus	oesophagus
8	chr11:4038800-4050000	Weak transcription	K562	blood
9	chr11:4039200-4056400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr11:4040200-4046800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:4040200-4049600	Weak transcription	A549	lung
12	chr11:4040400-4045600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr11:4040400-4046200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:4041000-4046600	Weak transcription	NHEK	skin
15	chr11:4041200-4046000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr11:4041400-4046200	Weak transcription	NHDF-Ad	bronchial
17	chr11:4041600-4045400	Weak transcription	Fetal Stomach	stomach
18	chr11:4041600-4046000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:4041600-4046800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr11:4041800-4054600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr11:4042000-4046000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr11:4042000-4046000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:4043000-4045600	Weak transcription	Fetal Lung	lung
24	chr11:4043400-4047000	Strong transcription	Primary T cells from cord blood	blood
25	chr11:4043400-4051200	Weak transcription	Liver	Liver
26	chr11:4043600-4046400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:4043600-4046400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:4043600-4048000	Strong transcription	Thymus	Thymus
29	chr11:4043600-4049400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr11:4043800-4046000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:4043800-4046000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr11:4044000-4045800	ZNF genes & repeats	GM12878-XiMat	blood
33	chr11:4044000-4046000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
34	chr11:4044000-4048200	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr11:4044200-4045800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
36	chr11:4044200-4047000	Weak transcription	Osteobl	bone
37	chr11:4044200-4047200	Weak transcription	Brain Hippocampus Middle	brain
38	chr11:4044200-4050200	Strong transcription	Fetal Thymus	thymus
39	chr11:4044400-4045600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr11:4044400-4046400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:4044400-4048200	Strong transcription	Dnd41	blood
42	chr11:4044400-4049200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr11:4044600-4045600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr11:4044600-4046400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:4044600-4048000	Weak transcription	Small Intestine	intestine
46	chr11:4044800-4045800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr11:4044800-4046600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr11:4044800-4049000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr11:4045000-4045600	Strong transcription	Colonic Mucosa	Colon
50	chr11:4045000-4045600	Enhancers	Ovary	ovary

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