Variant report

Variant	rs2956682
Chromosome Location	chr7:128212998-128212999
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1013514	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10225988	0.81[ASN][1000 genomes]
rs10954206	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11769769	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11982488	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28505422	0.81[ASN][1000 genomes]
rs4731481	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55817807	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55928948	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59287454	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60382581	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61437980	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62481896	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62481928	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62483311	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62483370	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6467200	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6955870	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6955960	0.81[ASN][1000 genomes]
rs6965333	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7795141	0.89[ASN][1000 genomes]
rs7795558	0.81[ASN][1000 genomes]
rs7800335	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7804825	0.81[ASN][1000 genomes]
rs9768325	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1848097	chr7:128179503-128248497	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv1810084	chr7:128201902-128248697	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv1829966	chr7:128201902-128248697	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1847512	chr7:128201902-128248697	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3478067	chr7:128209147-128216052	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
7	esv3478068	chr7:128209147-128216052	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
8	nsv966885	chr7:128212815-128256300	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs2956682	RP11-274B21.2	cis	Stomach	GTEx
rs2956682	RP11-274B21.4	cis	Stomach	GTEx
rs2956682	RP11-274B21.4	cis	Thyroid	GTEx
rs2956682	RP11-274B21.2	cis	lung	GTEx
rs2956682	RP11-274B21.1	cis	Nerve Tibial	GTEx
rs2956682	RP11-274B21.2	cis	Skin Sun Exposed Lower leg	GTEx
rs2956682	CICP14	cis	Thyroid	GTEx
rs2956682	RP11-274B21.4	cis	Esophagus Mucosa	GTEx
rs2956682	RP11-274B21.2	cis	Muscle Skeletal	GTEx
rs2956682	RP11-274B21.4	cis	Skin Sun Exposed Lower leg	GTEx
rs2956682	RP11-274B21.1	cis	Skin Sun Exposed Lower leg	GTEx
rs2956682	RP11-274B21.3	cis	Nerve Tibial	GTEx
rs2956682	RP11-274B21.3	cis	Muscle Skeletal	GTEx
rs2956682	RP11-274B21.2	cis	Nerve Tibial	GTEx
rs2956682	RP11-274B21.1	cis	lung	GTEx
rs2956682	RP11-274B21.4	cis	Adipose Subcutaneous	GTEx
rs2956682	RP11-274B21.2	cis	Thyroid	GTEx
rs2956682	CICP14	cis	Skin Sun Exposed Lower leg	GTEx
rs2956682	RP11-274B21.4	cis	lung	GTEx
rs2956682	RP11-274B21.2	cis	Adipose Subcutaneous	GTEx
rs2956682	RP11-274B21.4	cis	Muscle Skeletal	GTEx
rs2956682	RP11-274B21.3	cis	Thyroid	GTEx
rs2956682	RP11-274B21.4	cis	Nerve Tibial	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128172600-128214800	Weak transcription	Gastric	stomach
2	chr7:128172800-128239800	Weak transcription	Small Intestine	intestine
3	chr7:128173000-128231800	Weak transcription	Colonic Mucosa	Colon
4	chr7:128173000-128231800	Weak transcription	Fetal Kidney	kidney
5	chr7:128173600-128214800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:128173800-128214800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr7:128173800-128234400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:128174000-128220600	Weak transcription	NHLF	lung
9	chr7:128174000-128231800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:128174000-128232600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:128175400-128231800	Weak transcription	Left Ventricle	heart
12	chr7:128176000-128214800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:128177600-128231800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr7:128179200-128231800	Weak transcription	Esophagus	oesophagus
15	chr7:128181800-128231800	Weak transcription	Aorta	Aorta
16	chr7:128183000-128214200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:128183400-128214800	Weak transcription	HUVEC	blood vessel
18	chr7:128183600-128214800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr7:128187400-128214800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr7:128187400-128214800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:128187600-128213800	Weak transcription	Osteobl	bone
22	chr7:128187600-128214400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr7:128187600-128232000	Weak transcription	NH-A	brain
24	chr7:128187800-128214800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr7:128188000-128213800	Weak transcription	Brain Anterior Caudate	brain
26	chr7:128188000-128213800	Weak transcription	Brain Hippocampus Middle	brain
27	chr7:128188000-128214800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr7:128188000-128214800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr7:128188000-128215000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:128188000-128215000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:128188000-128220800	Weak transcription	NHEK	skin
32	chr7:128188000-128232800	Weak transcription	Fetal Brain Female	brain
33	chr7:128188200-128215000	Weak transcription	Hela-S3	cervix
34	chr7:128188200-128229800	Weak transcription	HSMM	muscle
35	chr7:128188400-128214800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr7:128188400-128230800	Weak transcription	Primary T cells from cord blood	blood
37	chr7:128188400-128231200	Weak transcription	Pancreas	Pancrea
38	chr7:128188600-128213800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr7:128188800-128231800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr7:128189200-128220400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr7:128190600-128220400	Weak transcription	NHDF-Ad	bronchial
42	chr7:128191200-128226000	Weak transcription	Ovary	ovary
43	chr7:128191400-128220600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr7:128191400-128232000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:128191600-128215000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr7:128191800-128213600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr7:128197800-128241800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr7:128199400-128231800	Weak transcription	HSMMtube	muscle
49	chr7:128199800-128214200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr7:128199800-128214200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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