Variant report

Variant	rs769211
Chromosome Location	chr1:94360107-94360108
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	chr1:94344004..94346272-chr1:94357080..94360433,6	K562	blood:

Variant related genes	Relation type
ENSG00000067334	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10159000	0.97[ASN][1000 genomes]
rs10489607	0.97[ASN][1000 genomes]
rs10874809	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs10874811	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs10874812	0.97[ASN][1000 genomes]
rs11165004	0.93[JPT][hapmap]
rs11165006	0.93[JPT][hapmap]
rs11165007	0.93[JPT][hapmap]
rs11165030	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs11165031	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165034	0.97[ASN][1000 genomes]
rs11165037	0.94[ASN][1000 genomes]
rs12068168	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12068345	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12089163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122176	1.00[JPT][hapmap]
rs12122406	0.94[ASN][1000 genomes]
rs12125068	0.93[JPT][hapmap]
rs12126518	0.80[CHD][hapmap]
rs12129986	0.95[ASN][1000 genomes]
rs12130623	0.95[ASN][1000 genomes]
rs12131163	0.94[ASN][1000 genomes]
rs12131247	0.97[ASN][1000 genomes]
rs12134159	0.93[JPT][hapmap]
rs12135187	0.93[JPT][hapmap]
rs12135991	0.97[ASN][1000 genomes]
rs12139561	0.93[JPT][hapmap]
rs12140014	0.93[JPT][hapmap]
rs12140097	0.94[ASN][1000 genomes]
rs12141697	0.89[JPT][hapmap]
rs12142384	0.93[JPT][hapmap]
rs12144277	0.86[JPT][hapmap]
rs12401354	0.91[ASN][1000 genomes]
rs12404613	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs12406885	0.93[JPT][hapmap]
rs12407732	0.93[JPT][hapmap]
rs12410342	0.93[JPT][hapmap]
rs12410985	0.84[CHB][hapmap]
rs1473711	0.97[ASN][1000 genomes]
rs17100392	0.80[CHD][hapmap];0.93[JPT][hapmap]
rs1852	0.90[CHB][hapmap]
rs1989020	0.97[ASN][1000 genomes]
rs1989021	0.97[ASN][1000 genomes]
rs2017736	0.97[ASN][1000 genomes]
rs2092697	0.94[ASN][1000 genomes]
rs2143993	0.94[ASN][1000 genomes]
rs2273406	0.94[ASN][1000 genomes]
rs2391324	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3170633	0.84[CHB][hapmap]
rs35674584	0.95[ASN][1000 genomes]
rs3761912	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs3827715	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41303970	0.94[ASN][1000 genomes]
rs4573532	0.94[ASN][1000 genomes]
rs4598495	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57387172	0.97[ASN][1000 genomes]
rs60120441	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61667071	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680027	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681078	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687387	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs6688926	0.93[JPT][hapmap]
rs6696758	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs6699912	0.97[ASN][1000 genomes]
rs6700112	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718873	0.97[ASN][1000 genomes]
rs718874	0.97[ASN][1000 genomes]
rs718875	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs743119	0.94[ASN][1000 genomes]
rs7515191	0.82[JPT][hapmap]
rs7517826	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7533596	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs7536714	0.97[ASN][1000 genomes]
rs7544883	0.93[JPT][hapmap]
rs7546315	0.93[JPT][hapmap]
rs7549683	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs761889	0.97[ASN][1000 genomes]
rs960625	0.93[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523355	chr1:94351328-94385591	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs769211	GCLM	cis	parietal	SCAN
rs769211	GCLM	Cis_1M	lymphoblastoid	RTeQTL
rs769211	GCLM	cis	uninvolved skin	skin_eQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94345000-94374200	Weak transcription	Gastric	stomach
2	chr1:94345000-94374200	Weak transcription	Spleen	Spleen
3	chr1:94345200-94374000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:94345200-94374200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:94345400-94361000	Weak transcription	Fetal Thymus	thymus
6	chr1:94345400-94362000	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:94345400-94364000	Weak transcription	Fetal Intestine Small	intestine
8	chr1:94345400-94369400	Weak transcription	Colonic Mucosa	Colon
9	chr1:94345400-94373200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:94345400-94373200	Weak transcription	Brain Substantia Nigra	brain
11	chr1:94345400-94373800	Weak transcription	Fetal Stomach	stomach
12	chr1:94345400-94374000	Weak transcription	Right Ventricle	heart
13	chr1:94345600-94361000	Weak transcription	Brain Angular Gyrus	brain
14	chr1:94345600-94361000	Weak transcription	Brain Anterior Caudate	brain
15	chr1:94345600-94361800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:94345600-94362000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:94345600-94362000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:94345600-94362000	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:94345600-94369400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:94345600-94369400	Weak transcription	Fetal Lung	lung
21	chr1:94345600-94369800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:94345600-94371600	Weak transcription	Fetal Kidney	kidney
23	chr1:94345600-94373000	Weak transcription	Fetal Brain Female	brain
24	chr1:94345600-94373200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:94345600-94373200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:94345600-94373200	Weak transcription	Fetal Brain Male	brain
27	chr1:94345600-94373400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:94345600-94373400	Weak transcription	Psoas Muscle	Psoas
29	chr1:94345600-94373400	Weak transcription	Stomach Mucosa	stomach
30	chr1:94345600-94373600	Weak transcription	Brain Germinal Matrix	brain
31	chr1:94345800-94362000	Weak transcription	HSMMtube	muscle
32	chr1:94345800-94366000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:94345800-94369200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:94345800-94371200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:94347400-94374200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:94347600-94367600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:94350400-94367200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:94350600-94369400	Strong transcription	HMEC	breast
39	chr1:94351200-94364600	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr1:94351200-94367400	Strong transcription	Liver	Liver
41	chr1:94351600-94362000	Weak transcription	Ovary	ovary
42	chr1:94352800-94370400	Weak transcription	Lung	lung
43	chr1:94352800-94373000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:94353000-94361800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:94353000-94367400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:94353600-94363400	Strong transcription	Dnd41	blood
47	chr1:94353600-94367200	Strong transcription	Osteobl	bone
48	chr1:94353600-94368200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:94353800-94367200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:94354200-94370400	Weak transcription	Small Intestine	intestine

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