Variant report

Variant	rs11602757
Chromosome Location	chr11:4053881-4053882
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10160649	0.82[LWK][hapmap]
rs10742229	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10767827	0.86[YRI][hapmap]
rs11030814	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1442725	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1465952	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2060822	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2289570	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2412341	0.86[CHB][hapmap]
rs2898950	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2920137	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2920140	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2920141	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2920142	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2923946	0.90[GIH][hapmap];0.88[MKK][hapmap]
rs2923947	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2923951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2923952	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2923954	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2959058	0.86[MKK][hapmap]
rs2959060	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959064	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2959069	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2959071	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2959072	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2959076	0.85[CHB][hapmap]
rs2959080	0.90[GIH][hapmap];0.89[MKK][hapmap]
rs35695744	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3794051	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3794052	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4910595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910881	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6578440	0.82[YRI][hapmap]
rs7109811	0.85[AMR][1000 genomes]
rs727152	0.90[GIH][hapmap];0.88[MKK][hapmap]
rs7924858	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7926908	0.83[EUR][1000 genomes]
rs7927493	0.90[EUR][1000 genomes]
rs7930739	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7938946	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7940635	0.86[EUR][1000 genomes]
rs7945918	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs894455	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs894457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9735835	0.81[EUR][1000 genomes]
rs9988893	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11602757	C11orf21	cis	parietal	SCAN
rs11602757	OR5E1P	cis	parietal	SCAN
rs11602757	RRM1	cis	cerebellum	SCAN
rs11602757	OR52E4	cis	parietal	SCAN
rs11602757	IFITM5	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4038200-4057200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:4038200-4065200	Weak transcription	Left Ventricle	heart
3	chr11:4038400-4065400	Weak transcription	Esophagus	oesophagus
4	chr11:4039200-4056400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr11:4041800-4054600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:4046000-4061400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr11:4047400-4055400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr11:4047400-4061400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr11:4047800-4077400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:4048000-4060000	Weak transcription	NHDF-Ad	bronchial
11	chr11:4048000-4077600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:4048400-4054400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr11:4048400-4054800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr11:4048400-4061400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr11:4048400-4061800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr11:4048400-4062000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:4048400-4063200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:4048400-4065800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr11:4048600-4077800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:4049600-4070600	Weak transcription	Thymus	Thymus
21	chr11:4049800-4065400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr11:4050200-4070800	Weak transcription	Fetal Thymus	thymus
23	chr11:4051000-4080400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:4051200-4070200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr11:4051400-4065400	Weak transcription	Pancreas	Pancrea
26	chr11:4052200-4054600	Weak transcription	Liver	Liver
27	chr11:4052800-4054000	Strong transcription	Primary B cells from cord blood	blood
28	chr11:4053400-4054000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
29	chr11:4053800-4059600	Weak transcription	Primary T cells from cord blood	blood

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