Variant report

Variant	rs10835454
Chromosome Location	chr11:4013149-4013150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1013351	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10500590	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767702	0.84[EUR][1000 genomes]
rs10767713	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10767715	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10767767	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10767811	0.80[EUR][1000 genomes]
rs10835311	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10835312	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10835331	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10835340	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10835359	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835399	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835402	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835403	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835406	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835407	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835474	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835508	0.87[EUR][1000 genomes]
rs10835521	0.81[EUR][1000 genomes]
rs10835556	0.87[EUR][1000 genomes]
rs10835557	0.88[EUR][1000 genomes]
rs10835561	0.80[ASN][1000 genomes]
rs10835596	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835597	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835601	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835604	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11030276	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11030579	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11030599	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11030627	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11030631	0.90[EUR][1000 genomes]
rs11030639	0.88[EUR][1000 genomes]
rs11030660	0.91[EUR][1000 genomes]
rs11493482	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12223176	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12281293	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12283447	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12286710	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12290747	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12295138	0.81[EUR][1000 genomes]
rs1349583	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1442726	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1452047	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17081	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17279635	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2119987	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2898947	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4910590	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4910596	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4910597	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4910598	0.84[EUR][1000 genomes]
rs4910866	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4910868	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4910869	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4910875	0.91[EUR][1000 genomes]
rs4910877	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4910880	0.80[ASN][1000 genomes]
rs66503725	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66596383	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67065286	0.82[EUR][1000 genomes]
rs67300156	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7102215	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7128762	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs714380	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71466139	0.81[ASN][1000 genomes]
rs720571	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7935824	0.90[EUR][1000 genomes]
rs7950153	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs963998	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs995498	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv971974	chr11:4009259-4018790	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10835454	STIM1	cis	lung	GTEx
rs10835454	RRM1	cis	Thyroid	GTEx
rs10835454	RRM1	cis	Artery Tibial	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3989400-4031000	Weak transcription	Aorta	Aorta
2	chr11:3994400-4016600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:4003200-4016600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:4006200-4013800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr11:4006400-4016600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:4006800-4022600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:4007200-4013800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr11:4007200-4014000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr11:4007800-4015000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:4008600-4015400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr11:4009000-4013800	Weak transcription	Primary B cells from cord blood	blood
12	chr11:4009400-4017400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:4009400-4020200	Weak transcription	Pancreas	Pancrea
14	chr11:4009600-4017200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr11:4010800-4015800	Weak transcription	Left Ventricle	heart
16	chr11:4010800-4015800	Weak transcription	Thymus	Thymus
17	chr11:4010800-4017200	Weak transcription	Fetal Thymus	thymus
18	chr11:4011200-4014400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr11:4011200-4014400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:4011400-4013200	Weak transcription	A549	lung
21	chr11:4011600-4015000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr11:4011800-4013800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:4011800-4014000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr11:4011800-4014000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr11:4011800-4027600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:4012000-4014000	Weak transcription	Primary T cells from cord blood	blood
27	chr11:4012200-4015400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr11:4012600-4013200	Weak transcription	K562	blood
29	chr11:4012800-4013800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr11:4012800-4013800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr11:4012800-4015200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:4012800-4016600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:4013000-4016600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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