Variant report

Variant	rs2171668
Chromosome Location	chr11:46466828-46466829
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:46461604..46463369-chr11:46465505..46467389,2	K562	blood:
2	chr11:46461604..46464506-chr11:46464583..46467005,4	K562	blood:

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10160701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10838602	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038900	0.98[EUR][1000 genomes]
rs11038906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11038927	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11819869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12272795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12283172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12292425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs12295266	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12573978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12574250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12574668	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12575519	0.98[EUR][1000 genomes]
rs12576115	0.94[EUR][1000 genomes]
rs12576317	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12576359	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12577142	0.95[EUR][1000 genomes]
rs12578042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1472001	0.83[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16938506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17197116	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2046768	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2067482	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2171667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279465	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2291487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864072	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864076	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2902858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34406563	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs35324223	0.86[EUR][1000 genomes]
rs35623865	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs3740974	0.98[EUR][1000 genomes]
rs3740977	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs3802888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3809047	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4307676	0.87[EUR][1000 genomes]
rs55657382	0.91[EUR][1000 genomes]
rs55661562	0.91[EUR][1000 genomes]
rs55750336	0.90[ASN][1000 genomes]
rs55896955	0.80[EUR][1000 genomes]
rs57535407	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58147945	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59319338	0.95[EUR][1000 genomes]
rs60722866	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs60932698	0.89[EUR][1000 genomes]
rs61882674	0.82[EUR][1000 genomes]
rs61882678	0.90[EUR][1000 genomes]
rs61882682	0.96[EUR][1000 genomes]
rs61882683	0.92[EUR][1000 genomes]
rs61882691	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61882701	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882702	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61882706	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61882709	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882710	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882711	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882712	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882720	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882743	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882746	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882748	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882750	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882756	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882757	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882758	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61884262	0.85[EUR][1000 genomes]
rs61884264	0.93[EUR][1000 genomes]
rs61884271	0.89[EUR][1000 genomes]
rs61884273	0.87[EUR][1000 genomes]
rs61884274	0.87[EUR][1000 genomes]
rs61884292	0.80[EUR][1000 genomes]
rs6485682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6485685	0.91[EUR][1000 genomes]
rs7108770	0.91[EUR][1000 genomes]
rs7109698	0.81[EUR][1000 genomes]
rs7112229	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7122039	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7125907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7126316	0.86[EUR][1000 genomes]
rs7126343	0.87[EUR][1000 genomes]
rs7127529	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7128092	0.86[EUR][1000 genomes]
rs7130141	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73449983	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7481312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7484002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes]
rs756343	0.90[ASN][1000 genomes]
rs7924401	0.92[EUR][1000 genomes]
rs7930103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs7936413	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7946705	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7951579	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951870	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs876701	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]

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	nsv554202	chr11:46334239-46469900	Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1050614	chr11:46414720-46496732	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2171668	ATG13	cis	parietal	SCAN
rs2171668	C11orf49	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46426800-46468800	Weak transcription	Psoas Muscle	Psoas
2	chr11:46451400-46467600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:46455200-46472200	Weak transcription	Ovary	ovary
4	chr11:46455200-46488800	Weak transcription	Hela-S3	cervix
5	chr11:46455400-46467400	Weak transcription	Stomach Mucosa	stomach
6	chr11:46455400-46492200	Weak transcription	A549	lung
7	chr11:46456400-46467200	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:46456400-46467200	Weak transcription	HMEC	breast
9	chr11:46456400-46468200	Weak transcription	Fetal Kidney	kidney
10	chr11:46456600-46469600	Weak transcription	Fetal Brain Female	brain
11	chr11:46456600-46493600	Weak transcription	Colonic Mucosa	Colon
12	chr11:46456800-46468200	Weak transcription	NHLF	lung
13	chr11:46456800-46494200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr11:46456800-46515000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr11:46457200-46472400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:46457600-46467600	Weak transcription	Right Ventricle	heart
17	chr11:46457800-46470200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr11:46458200-46477200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:46458800-46467600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr11:46460000-46467600	Weak transcription	HUVEC	blood vessel
21	chr11:46460200-46467600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:46460200-46468000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr11:46460400-46467600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr11:46460600-46467600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr11:46460800-46472600	Weak transcription	Small Intestine	intestine
26	chr11:46464000-46470000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr11:46464200-46467000	Weak transcription	Fetal Brain Male	brain
28	chr11:46464200-46467600	Weak transcription	Osteobl	bone
29	chr11:46464200-46468600	Weak transcription	Lung	lung
30	chr11:46464200-46472400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr11:46464200-46489200	Weak transcription	Thymus	Thymus
32	chr11:46464200-46489400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr11:46464200-46513000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr11:46464400-46467400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr11:46464400-46467600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:46464400-46489600	Weak transcription	Placenta	Placenta
37	chr11:46464600-46467600	Weak transcription	Aorta	Aorta
38	chr11:46464600-46468200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:46464600-46469000	Weak transcription	Pancreas	Pancrea
40	chr11:46464800-46467400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr11:46464800-46467600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:46464800-46468600	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr11:46464800-46478600	Weak transcription	Spleen	Spleen
44	chr11:46464800-46479000	Weak transcription	NHEK	skin
45	chr11:46465000-46467000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr11:46465000-46467400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr11:46465000-46467400	Weak transcription	HSMM	muscle
48	chr11:46465000-46467600	Weak transcription	Fetal Lung	lung
49	chr11:46465000-46468200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:46465000-46468400	Enhancers	Brain Cingulate Gyrus	brain

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