Variant report

Variant	rs6952866
Chromosome Location	chr7:39701218-39701219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11769865	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11982634	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2107710	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2158548	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2158549	0.89[EUR][1000 genomes]
rs2189837	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2329464	0.89[EUR][1000 genomes]
rs2876862	0.92[EUR][1000 genomes]
rs3823742	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4723887	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4723891	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4723892	0.89[EUR][1000 genomes]
rs6462936	0.87[EUR][1000 genomes]
rs6462937	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6952363	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6956681	0.89[EUR][1000 genomes]
rs6961667	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6969070	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6969523	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7785049	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7806651	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs917077	0.82[AFR][1000 genomes];0.91[EUR][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	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv887972	chr7:39666267-39733688	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6952866	LINC00265	cis	Thyroid	GTEx
rs6952866	LINC00265	cis	lung	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39672200-39722800	Weak transcription	Hela-S3	cervix
2	chr7:39675200-39708800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr7:39675600-39701400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr7:39680000-39721600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr7:39680800-39704200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:39680800-39716400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr7:39682000-39704000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:39682000-39704000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:39682600-39702600	Weak transcription	Gastric	stomach
10	chr7:39682800-39722000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr7:39683400-39716600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr7:39683600-39712600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr7:39686200-39704400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr7:39687400-39715000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr7:39688400-39702200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:39689200-39703800	Weak transcription	Psoas Muscle	Psoas
17	chr7:39690200-39706600	Weak transcription	Fetal Heart	heart
18	chr7:39691800-39707000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr7:39691800-39708800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr7:39692000-39707000	Weak transcription	Stomach Mucosa	stomach
21	chr7:39692000-39707000	Weak transcription	HSMMtube	muscle
22	chr7:39692000-39707200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr7:39692200-39714000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr7:39695000-39701400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr7:39695000-39701600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr7:39695200-39702600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr7:39696400-39701400	Weak transcription	Thymus	Thymus
28	chr7:39697600-39707000	Weak transcription	Adipose Nuclei	Adipose
29	chr7:39697800-39707000	Weak transcription	HSMM	muscle
30	chr7:39698000-39701400	Weak transcription	Right Ventricle	heart
31	chr7:39698000-39704400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:39698800-39707000	Weak transcription	Left Ventricle	heart
33	chr7:39699000-39702000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
34	chr7:39699200-39705000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr7:39699400-39705800	Weak transcription	NHDF-Ad	bronchial
36	chr7:39699400-39707000	Weak transcription	Ovary	ovary
37	chr7:39699400-39712000	Weak transcription	Fetal Kidney	kidney
38	chr7:39699600-39702000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr7:39699600-39706400	Weak transcription	NHLF	lung
40	chr7:39699600-39707000	Weak transcription	Osteobl	bone
41	chr7:39699800-39702400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
42	chr7:39699800-39703200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:39700000-39703400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr7:39700000-39703400	ZNF genes & repeats	Primary T cells from cord blood	blood
45	chr7:39700000-39704400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr7:39700000-39707000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr7:39700000-39728200	Weak transcription	Liver	Liver
48	chr7:39700200-39703400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr7:39700400-39701800	Weak transcription	HUVEC	blood vessel
50	chr7:39700400-39702000	ZNF genes & repeats	Fetal Intestine Small	intestine

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