Variant report

Variant	rs10835402
Chromosome Location	chr11:3990914-3990915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1013351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10500590	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10742200	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs10767702	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10767713	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767767	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10767811	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10835239	0.86[CEU][hapmap]
rs10835311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835312	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835337	0.85[EUR][1000 genomes]
rs10835340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835359	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10835390	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs10835399	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835403	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]
rs10835406	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835454	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835474	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10835508	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835521	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835540	0.83[CEU][hapmap];0.94[CHB][hapmap]
rs10835556	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10835557	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10835561	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10835596	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835597	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835601	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835604	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11030276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11030404	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs11030579	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11030599	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11030627	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11030631	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11030639	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11030660	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11030781	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11493482	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1155146	0.83[CEU][hapmap]
rs11828337	0.85[EUR][1000 genomes]
rs12223176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12281293	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12283447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12286710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12290747	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12295138	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1349583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1442726	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1452047	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1452048	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs17081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1839910	0.86[EUR][1000 genomes]
rs2119987	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2412338	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs28419002	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2898947	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];0.98[ASN][1000 genomes]
rs4910590	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910596	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4910597	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4910598	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4910866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910869	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4910875	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4910877	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4910880	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6578424	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs66503725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66596383	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67065286	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67300156	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7102215	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7113845	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs7128762	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs714380	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71466139	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs718937	1.00[YRI][hapmap]
rs720571	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7924984	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs7925954	0.83[EUR][1000 genomes]
rs7935824	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7950153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs963998	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs995498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10835402	RRM1	cis	Artery Tibial	GTEx
rs10835402	STIM1	cis	lung	GTEx
rs10835402	RRM1	cis	Thyroid	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3961200-4002000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:3973200-3993200	Weak transcription	Colon Smooth Muscle	Colon
3	chr11:3973200-4008400	Weak transcription	Fetal Lung	lung
4	chr11:3973600-3993800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:3975000-4006000	Weak transcription	Right Ventricle	heart
6	chr11:3980600-3994200	Weak transcription	Fetal Stomach	stomach
7	chr11:3981600-3993000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr11:3982000-3993200	Weak transcription	NHEK	skin
9	chr11:3982400-3994200	Weak transcription	Brain Anterior Caudate	brain
10	chr11:3982600-3992800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:3982600-3994000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:3982600-3994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr11:3982600-4004400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:3982600-4005600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr11:3982600-4006000	Weak transcription	Left Ventricle	heart
16	chr11:3983600-3992000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr11:3984000-4010400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:3984400-3993000	Weak transcription	A549	lung
19	chr11:3984800-3991800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr11:3985000-3993000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:3985000-3993200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:3985000-4002400	Weak transcription	NHDF-Ad	bronchial
23	chr11:3985800-3993800	Weak transcription	HMEC	breast
24	chr11:3985800-4001200	Weak transcription	Small Intestine	intestine
25	chr11:3986000-4008000	Weak transcription	HepG2	liver
26	chr11:3987000-4010400	Weak transcription	Fetal Intestine Small	intestine
27	chr11:3987200-4001600	Weak transcription	Gastric	stomach
28	chr11:3987800-3993400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr11:3988000-4002400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:3988200-3991800	Genic enhancers	Primary T cells from cord blood	blood
31	chr11:3988200-3991800	Weak transcription	Fetal Intestine Large	intestine
32	chr11:3988200-4006200	Weak transcription	Pancreas	Pancrea
33	chr11:3988400-3991800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr11:3988600-3991200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr11:3988600-3991600	Genic enhancers	Dnd41	blood
36	chr11:3988800-3991800	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr11:3989400-3991000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr11:3989400-3991000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:3989400-3992600	Weak transcription	Psoas Muscle	Psoas
40	chr11:3989400-3993400	Weak transcription	Lung	lung
41	chr11:3989400-3997600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr11:3989400-4010600	Weak transcription	Spleen	Spleen
43	chr11:3989400-4031000	Weak transcription	Aorta	Aorta
44	chr11:3989600-3991400	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr11:3989600-3991800	Genic enhancers	Thymus	Thymus
46	chr11:3989600-3992200	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr11:3989800-3991000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr11:3989800-3992200	Weak transcription	K562	blood
49	chr11:3989800-4002400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr11:3989800-4006000	Weak transcription	Rectal Smooth Muscle	rectum

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