Variant report

Variant	rs2237662
Chromosome Location	chr7:106874065-106874066
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:106869281..106872161-chr7:106872370..106874834,2	K562	blood:
2	chr7:106867953..106869939-chr7:106873583..106876575,2	K562	blood:
3	chr7:106872239..106874201-chr7:106876905..106879195,2	K562	blood:
4	chr7:106872926..106875366-chr7:106876350..106878360,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12670688	0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12672451	0.90[CEU][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13230144	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17153981	0.89[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2107317	0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2237659	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2237660	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2237661	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2237665	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2251838	0.81[MKK][hapmap]
rs2283038	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2301801	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2395868	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2395869	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2536501	0.81[MKK][hapmap]
rs3801964	0.90[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3801966	0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62483619	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62483627	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62483629	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62483633	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62483634	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62483640	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62483641	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7785892	0.87[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7803151	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS 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	31 gene(s)	inside rSNPs	diseases
2	nsv888939	chr7:106849393-107045700	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2756226	chr7:106850755-106944563	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2237662	COG5	cis	parietal	SCAN
rs2237662	GPR22	cis	multi-tissue	Pritchard

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106844600-106880400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr7:106844600-106888400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:106846000-106925800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr7:106850400-106890000	Weak transcription	Hela-S3	cervix
5	chr7:106850800-106895200	Weak transcription	Colon Smooth Muscle	Colon
6	chr7:106851000-106897600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr7:106851000-106946000	Weak transcription	Esophagus	oesophagus
8	chr7:106851200-106874800	Weak transcription	Ovary	ovary
9	chr7:106851200-106882200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:106851200-106888200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr7:106851200-106892400	Weak transcription	Gastric	stomach
12	chr7:106851200-106892600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:106853400-106925600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:106854400-106878000	Weak transcription	K562	blood
15	chr7:106855600-106883000	Weak transcription	Dnd41	blood
16	chr7:106857200-106877000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr7:106860200-106882600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr7:106861600-106876200	Weak transcription	Fetal Brain Female	brain
19	chr7:106863800-106887400	Weak transcription	Thymus	Thymus
20	chr7:106864000-106875800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr7:106864000-106878400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:106864000-106889600	Weak transcription	Spleen	Spleen
23	chr7:106865000-106887000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr7:106865200-106884400	Weak transcription	Fetal Muscle Leg	muscle
25	chr7:106865400-106884400	Weak transcription	Fetal Thymus	thymus
26	chr7:106865600-106874400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr7:106865600-106876200	Weak transcription	Fetal Intestine Large	intestine
28	chr7:106865600-106877400	Weak transcription	Brain Angular Gyrus	brain
29	chr7:106865600-106888200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr7:106865600-106890600	Weak transcription	Aorta	Aorta
31	chr7:106865600-106892400	Weak transcription	HepG2	liver
32	chr7:106865800-106874400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr7:106865800-106882600	Weak transcription	Lung	lung
34	chr7:106866000-106879000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr7:106866600-106874800	Weak transcription	Fetal Intestine Small	intestine
36	chr7:106866600-106882400	Weak transcription	Fetal Stomach	stomach
37	chr7:106866600-106909600	Weak transcription	Placenta	Placenta
38	chr7:106866800-106884600	Weak transcription	Liver	Liver
39	chr7:106867000-106888000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr7:106867600-106877200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr7:106867800-106884400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr7:106867800-106884600	Weak transcription	Adipose Nuclei	Adipose
43	chr7:106867800-106889800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr7:106868400-106883000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:106869000-106875800	Enhancers	NHEK	skin
46	chr7:106869600-106875000	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr7:106870400-106874800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr7:106870800-106887600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr7:106871000-106875400	Enhancers	HMEC	breast
50	chr7:106871200-106874400	Weak transcription	Primary monocytes fromperipheralblood	blood

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