Variant report

Variant	rs61782165
Chromosome Location	chr1:94356377-94356378
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94338439..94340228-chr1:94354900..94357420,2	K562	blood:
2	chr1:94343706..94346474-chr1:94354724..94357887,3	MCF-7	breast:
3	chr1:94349522..94351991-chr1:94354138..94356917,3	K562	blood:
4	chr1:94349796..94351991-chr1:94353690..94356917,3	K562	blood:

Variant related genes	Relation type
ENSG00000067334	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10489605	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10874795	0.81[ASN][1000 genomes]
rs11164994	0.85[EUR][1000 genomes]
rs11165019	0.81[ASN][1000 genomes]
rs12079584	0.81[ASN][1000 genomes]
rs12239830	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17100397	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17304770	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17878271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17878294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17881810	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17884788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17885151	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17886352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223908	0.87[EUR][1000 genomes]
rs3761913	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41292665	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57870303	0.85[EUR][1000 genomes]
rs61425457	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61781049	0.83[EUR][1000 genomes]
rs61781051	0.85[EUR][1000 genomes]
rs61781053	0.87[EUR][1000 genomes]
rs61781054	0.85[EUR][1000 genomes]
rs61781055	0.85[EUR][1000 genomes]
rs61781056	0.85[EUR][1000 genomes]
rs61781057	0.87[EUR][1000 genomes]
rs61782162	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782163	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782164	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782167	0.86[ASN][1000 genomes]
rs61782398	0.85[EUR][1000 genomes]
rs61782399	0.85[EUR][1000 genomes]
rs61782400	0.87[EUR][1000 genomes]
rs61782403	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782404	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782405	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782410	0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782413	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782449	0.88[EUR][1000 genomes]
rs61782450	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782451	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61782458	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782459	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674149	0.80[EUR][1000 genomes]
rs72723114	0.85[EUR][1000 genomes]
rs72723118	0.86[EUR][1000 genomes]
rs72723125	0.87[EUR][1000 genomes]
rs72723138	0.85[EUR][1000 genomes]
rs72723157	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72723165	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72723169	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72723178	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723192	0.94[ASN][1000 genomes]
rs72967397	0.81[ASN][1000 genomes]
rs7523682	0.83[EUR][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61782165	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94345000-94357000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:94345000-94374200	Weak transcription	Gastric	stomach
3	chr1:94345000-94374200	Weak transcription	Spleen	Spleen
4	chr1:94345200-94358800	Weak transcription	Left Ventricle	heart
5	chr1:94345200-94374000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:94345200-94374200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:94345400-94356600	Weak transcription	Aorta	Aorta
8	chr1:94345400-94356800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:94345400-94357000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:94345400-94357200	Weak transcription	NHLF	lung
11	chr1:94345400-94358800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:94345400-94359200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:94345400-94361000	Weak transcription	Fetal Thymus	thymus
14	chr1:94345400-94362000	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:94345400-94364000	Weak transcription	Fetal Intestine Small	intestine
16	chr1:94345400-94369400	Weak transcription	Colonic Mucosa	Colon
17	chr1:94345400-94373200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:94345400-94373200	Weak transcription	Brain Substantia Nigra	brain
19	chr1:94345400-94373800	Weak transcription	Fetal Stomach	stomach
20	chr1:94345400-94374000	Weak transcription	Right Ventricle	heart
21	chr1:94345600-94357600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:94345600-94357800	Weak transcription	Hela-S3	cervix
23	chr1:94345600-94358400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr1:94345600-94358400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:94345600-94358600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:94345600-94358600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:94345600-94358600	Weak transcription	Fetal Intestine Large	intestine
28	chr1:94345600-94358600	Weak transcription	NHEK	skin
29	chr1:94345600-94358800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:94345600-94359400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:94345600-94359400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:94345600-94359400	Weak transcription	GM12878-XiMat	blood
33	chr1:94345600-94359600	Weak transcription	Primary B cells from cord blood	blood
34	chr1:94345600-94359600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:94345600-94361000	Weak transcription	Brain Angular Gyrus	brain
36	chr1:94345600-94361000	Weak transcription	Brain Anterior Caudate	brain
37	chr1:94345600-94361800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:94345600-94362000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:94345600-94362000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:94345600-94362000	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:94345600-94369400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr1:94345600-94369400	Weak transcription	Fetal Lung	lung
43	chr1:94345600-94369800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:94345600-94371600	Weak transcription	Fetal Kidney	kidney
45	chr1:94345600-94373000	Weak transcription	Fetal Brain Female	brain
46	chr1:94345600-94373200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:94345600-94373200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:94345600-94373200	Weak transcription	Fetal Brain Male	brain
49	chr1:94345600-94373400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:94345600-94373400	Weak transcription	Psoas Muscle	Psoas

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