Variant report

Variant	rs11691939
Chromosome Location	chr2:32339561-32339562
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:32317095..32319080-chr2:32338095..32340081,2	K562	blood:
2	chr2:32338831..32341439-chr2:32391344..32393556,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11124272	0.85[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap]
rs11678119	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs11683760	0.81[AMR][1000 genomes]
rs12478134	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs12614686	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs12618002	0.81[AMR][1000 genomes]
rs12991444	0.86[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap]
rs12996943	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13006495	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13006880	0.81[EUR][1000 genomes]
rs13007972	0.81[AMR][1000 genomes]
rs13013695	0.85[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17011801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs177082	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs186135	0.80[EUR][1000 genomes]
rs212682	0.86[EUR][1000 genomes]
rs212684	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs212689	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs212690	0.84[EUR][1000 genomes]
rs212691	0.84[EUR][1000 genomes]
rs212696	0.84[EUR][1000 genomes]
rs212710	0.80[EUR][1000 genomes]
rs212736	0.93[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap]
rs212742	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs212747	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs212751	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs212754	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs212761	0.93[CEU][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2280968	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2294178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2366547	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs34197800	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34835885	0.83[EUR][1000 genomes]
rs35978916	0.85[EUR][1000 genomes]
rs375050	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3752916	0.82[CEU][hapmap]
rs3754835	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs3769602	0.82[CEU][hapmap]
rs3769605	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs385076	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs3851310	0.82[CEU][hapmap]
rs410469	0.92[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4530415	0.82[ASN][1000 genomes]
rs462878	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4952207	0.85[ASN][1000 genomes]
rs56322034	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6543648	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6723154	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs6725184	0.83[CHB][hapmap]
rs6756085	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs686005	0.80[EUR][1000 genomes]
rs7556942	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7562653	0.92[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7572964	0.82[CEU][hapmap]
rs7574000	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7592239	0.81[AMR][1000 genomes]
rs7604289	0.82[AMR][1000 genomes]
rs805831	0.81[EUR][1000 genomes]
rs9789593	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[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	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv833670	chr2:32295778-32481857	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv873778	chr2:32297984-32409007	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv873779	chr2:32330885-32372245	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv817386	chr2:32332893-32724794	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1001038	chr2:32333378-32657112	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1009359	chr2:32333378-32725117	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv535613	chr2:32333378-32725117	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11691939	SLC30A6	cis	cerebellum	SCAN
rs11691939	SLC30A6	cis	parietal	SCAN
rs11691939	NLRC4	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:32290400-32353400	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:32292000-32343200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:32292600-32353800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:32295800-32353800	Weak transcription	Fetal Brain Male	brain
5	chr2:32296400-32362600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:32297600-32360600	Weak transcription	Osteobl	bone
7	chr2:32298800-32341400	Weak transcription	Small Intestine	intestine
8	chr2:32300000-32339600	Weak transcription	HepG2	liver
9	chr2:32309800-32381200	Weak transcription	NHDF-Ad	bronchial
10	chr2:32313200-32360600	Weak transcription	NH-A	brain
11	chr2:32316000-32353600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:32316200-32343200	Weak transcription	HSMM	muscle
13	chr2:32322200-32353400	Weak transcription	K562	blood
14	chr2:32325400-32353800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:32326000-32352200	Weak transcription	HSMMtube	muscle
16	chr2:32331200-32341000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:32331200-32370000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:32331400-32341200	Weak transcription	Stomach Mucosa	stomach
19	chr2:32331400-32368600	Weak transcription	Psoas Muscle	Psoas
20	chr2:32331400-32370000	Weak transcription	Right Ventricle	heart
21	chr2:32331600-32341000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:32331600-32341600	Weak transcription	Aorta	Aorta
23	chr2:32331600-32341600	Weak transcription	Esophagus	oesophagus
24	chr2:32331600-32343600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:32331600-32343600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:32331600-32344000	Weak transcription	Brain Angular Gyrus	brain
27	chr2:32331600-32353600	Weak transcription	Brain Substantia Nigra	brain
28	chr2:32331600-32353600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:32331600-32353800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:32331600-32353800	Weak transcription	Brain Anterior Caudate	brain
31	chr2:32331600-32354400	Weak transcription	Colonic Mucosa	Colon
32	chr2:32331600-32354600	Weak transcription	Spleen	Spleen
33	chr2:32331600-32377400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:32331600-32390200	Weak transcription	Gastric	stomach
35	chr2:32331600-32390200	Weak transcription	Pancreas	Pancrea
36	chr2:32331800-32340800	Weak transcription	Placenta	Placenta
37	chr2:32331800-32341600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:32331800-32343800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:32331800-32344000	Weak transcription	Colon Smooth Muscle	Colon
40	chr2:32331800-32350400	Weak transcription	Lung	lung
41	chr2:32331800-32351000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:32331800-32353400	Weak transcription	Fetal Kidney	kidney
43	chr2:32331800-32353600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr2:32331800-32360600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:32331800-32376400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr2:32332000-32339800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:32332000-32341200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:32332000-32353800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:32332200-32341600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr2:32332200-32342800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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