Variant report

Variant	rs2303608
Chromosome Location	chr2:231307860-231307861
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1074886	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11675127	0.87[ASN][1000 genomes]
rs11675135	0.87[ASN][1000 genomes]
rs11676089	0.87[ASN][1000 genomes]
rs11676310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11677269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677512	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];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677646	0.85[ASN][1000 genomes]
rs11679026	0.85[ASN][1000 genomes]
rs11681234	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11681358	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11687964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11688362	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11688458	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11692506	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11692527	0.87[ASN][1000 genomes]
rs11692602	0.87[ASN][1000 genomes]
rs11693767	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11694346	0.93[ASN][1000 genomes]
rs11694422	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11694428	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11695277	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];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694865	0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1427284	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17273079	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17332171	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17332742	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17333189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35919859	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3752431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3754940	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3754941	0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3754942	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3754943	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3769849	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3815885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893836	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs55637456	0.93[ASN][1000 genomes]
rs55770359	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55893188	0.85[ASN][1000 genomes]
rs55964110	0.87[ASN][1000 genomes]
rs56007282	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56044062	0.87[ASN][1000 genomes]
rs56052963	0.87[ASN][1000 genomes]
rs56105857	0.87[ASN][1000 genomes]
rs56108366	0.87[ASN][1000 genomes]
rs56251216	0.87[ASN][1000 genomes]
rs56303947	0.87[ASN][1000 genomes]
rs56372741	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56401027	0.85[ASN][1000 genomes]
rs6436933	0.87[ASN][1000 genomes]
rs6706167	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6713447	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6713465	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6722656	0.90[ASN][1000 genomes]
rs6725726	0.90[ASN][1000 genomes]
rs6732684	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6732940	0.87[ASN][1000 genomes]
rs6748339	0.87[ASN][1000 genomes]
rs6748445	0.87[ASN][1000 genomes]
rs6750712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753500	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6759292	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761255	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs68096532	0.93[ASN][1000 genomes]
rs72495174	0.87[ASN][1000 genomes]
rs72495175	0.87[ASN][1000 genomes]
rs72495176	0.87[ASN][1000 genomes]
rs72495180	0.87[ASN][1000 genomes]
rs72495181	0.87[ASN][1000 genomes]
rs72495182	0.87[ASN][1000 genomes]
rs72495183	0.93[ASN][1000 genomes]
rs72495185	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs725202	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs72994332	0.85[ASN][1000 genomes]
rs72996270	0.85[ASN][1000 genomes]
rs72996292	0.87[ASN][1000 genomes]
rs72998203	0.87[ASN][1000 genomes]
rs72998264	0.93[ASN][1000 genomes]
rs72998283	0.93[ASN][1000 genomes]
rs73000239	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73000253	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73000268	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559665	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7563909	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7568128	0.93[ASN][1000 genomes]
rs7585646	0.87[ASN][1000 genomes]
rs7585731	0.87[ASN][1000 genomes]
rs7589948	0.87[ASN][1000 genomes]
rs7597033	0.87[ASN][1000 genomes]
rs7606804	0.93[ASN][1000 genomes]
rs999888	1.00[JPT][hapmap];0.93[ASN][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	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv584672	chr2:231289976-231348888	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2303608	TRPM8	cis	cerebellum	SCAN
rs2303608	SP140L	cis	lymphoblastoid	seeQTL
rs2303608	SP140L	cis	parietal	SCAN
rs2303608	LOC93349	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231283600-231309200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:231288800-231319000	Weak transcription	Fetal Kidney	kidney
3	chr2:231288800-231356000	Weak transcription	Stomach Mucosa	stomach
4	chr2:231289000-231309200	Weak transcription	Aorta	Aorta
5	chr2:231294200-231309600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:231294200-231311600	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:231295200-231309200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:231295800-231309000	Weak transcription	Small Intestine	intestine
9	chr2:231296000-231309400	Weak transcription	Colonic Mucosa	Colon
10	chr2:231296000-231310400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:231296200-231308400	Weak transcription	Gastric	stomach
12	chr2:231296200-231309200	Weak transcription	Fetal Stomach	stomach
13	chr2:231296200-231309200	Weak transcription	Spleen	Spleen
14	chr2:231299600-231308200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:231301400-231308400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:231301400-231309200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:231301400-231309200	Weak transcription	Lung	lung
18	chr2:231301400-231309200	Weak transcription	Ovary	ovary
19	chr2:231301400-231309200	Weak transcription	Pancreas	Pancrea
20	chr2:231301400-231314400	Weak transcription	Psoas Muscle	Psoas
21	chr2:231301800-231308000	Weak transcription	Placenta	Placenta
22	chr2:231301800-231309200	Weak transcription	Fetal Lung	lung
23	chr2:231301800-231312000	Weak transcription	HepG2	liver
24	chr2:231301800-231345000	Weak transcription	A549	lung
25	chr2:231302600-231308000	Weak transcription	Fetal Intestine Small	intestine
26	chr2:231303200-231317200	Genic enhancers	Primary B cells from peripheral blood	blood
27	chr2:231304200-231308200	Weak transcription	Fetal Intestine Large	intestine
28	chr2:231304200-231309200	Weak transcription	Right Ventricle	heart
29	chr2:231304400-231320800	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:231306000-231314400	Weak transcription	Esophagus	oesophagus
31	chr2:231306600-231308000	Weak transcription	HMEC	breast
32	chr2:231306600-231309200	Weak transcription	NH-A	brain
33	chr2:231306600-231309400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:231306600-231310400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:231306600-231312000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr2:231306600-231323400	Weak transcription	K562	blood
37	chr2:231306800-231308000	Weak transcription	HSMM	muscle
38	chr2:231306800-231311600	Genic enhancers	GM12878-XiMat	blood
39	chr2:231306800-231311800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr2:231306800-231318200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:231307000-231308000	Weak transcription	Adipose Nuclei	Adipose
42	chr2:231307200-231308000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
43	chr2:231307200-231308000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:231307200-231308600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:231307400-231308400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:231307400-231308600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr2:231307400-231309200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:231307400-231312600	Genic enhancers	Primary B cells from cord blood	blood
49	chr2:231307400-231317600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:231307400-231318200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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