Variant report

Variant	rs6710287
Chromosome Location	chr2:231231351-231231352
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1004868	1.00[CHB][hapmap]
rs1004869	1.00[CHB][hapmap]
rs10165012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170241	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12694864	1.00[CHB][hapmap]
rs12694867	1.00[CHD][hapmap]
rs12988385	1.00[CHB][hapmap]
rs13000381	1.00[CHB][hapmap]
rs13010639	1.00[CHB][hapmap]
rs13010998	1.00[CHB][hapmap]
rs13017297	1.00[CHB][hapmap]
rs13025209	1.00[CHB][hapmap]
rs13025520	1.00[CHB][hapmap]
rs13026323	1.00[CHB][hapmap]
rs13397985	1.00[CHD][hapmap]
rs13413034	1.00[CHD][hapmap]
rs1427293	1.00[CHB][hapmap]
rs1427294	1.00[CHB][hapmap]
rs1834748	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114585	1.00[CHB][hapmap]
rs2162478	1.00[CHB][hapmap]
rs2396745	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396746	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28445040	1.00[CHD][hapmap]
rs3948464	1.00[CHB][hapmap]
rs6707444	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6710297	1.00[CHD][hapmap]
rs6716753	1.00[CHD][hapmap]
rs6742304	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743984	1.00[CHD][hapmap]
rs7423615	1.00[CHD][hapmap]
rs9783992	1.00[CHB][hapmap]
rs9784019	1.00[CHB][hapmap]
rs9989899	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	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
3	esv3417154	chr2:231159789-231258938	Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3348338	chr2:231160124-231259498	Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv875945	chr2:231172642-231267925	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv869708	chr2:231173700-231267616	Genic enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1004183	chr2:231174420-231258603	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv3486129	chr2:231175581-231265831	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3486131	chr2:231175581-231265831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1013738	chr2:231176856-231258603	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv584667	chr2:231177822-231258450	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv460119	chr2:231178876-231258450	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv584668	chr2:231178876-231258450	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription 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	2 gene(s)	inside rSNPs	diseases
14	esv2751844	chr2:231179495-231280495	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv1001929	chr2:231179884-231258603	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1006206	chr2:231179884-231268938	Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv584669	chr2:231183321-231258150	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv584670	chr2:231183786-231241276	ZNF genes & repeats Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv875946	chr2:231184106-231277567	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	esv3374323	chr2:231186424-231244177	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv875947	chr2:231190446-231281286	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6710287	SP140	cis	lymphoblastoid	seeQTL
rs6710287	SCARNA6	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231212800-231235600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:231212800-231236600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:231212800-231253600	Weak transcription	Gastric	stomach
4	chr2:231212800-231253600	Weak transcription	HMEC	breast
5	chr2:231212800-231259200	Weak transcription	Small Intestine	intestine
6	chr2:231212800-231262400	Weak transcription	K562	blood
7	chr2:231213000-231237600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:231220000-231275800	Weak transcription	Stomach Mucosa	stomach
9	chr2:231222200-231253400	Weak transcription	Colonic Mucosa	Colon
10	chr2:231222200-231273200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:231222600-231233200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:231222800-231231600	Weak transcription	Fetal Intestine Small	intestine
13	chr2:231223200-231237600	Weak transcription	Right Ventricle	heart
14	chr2:231223200-231253600	Weak transcription	NHLF	lung
15	chr2:231223400-231235600	Weak transcription	NHDF-Ad	bronchial
16	chr2:231223400-231236200	Weak transcription	HUVEC	blood vessel
17	chr2:231223400-231237000	Weak transcription	NHEK	skin
18	chr2:231223400-231257800	Weak transcription	NH-A	brain
19	chr2:231223600-231263600	Weak transcription	Fetal Kidney	kidney
20	chr2:231224200-231254000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:231225200-231268000	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:231225600-231244600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:231226200-231231600	Weak transcription	Thymus	Thymus
24	chr2:231226600-231233800	Weak transcription	Esophagus	oesophagus
25	chr2:231226600-231233800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:231226600-231235400	Weak transcription	Osteobl	bone
27	chr2:231226600-231245600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:231226600-231253800	Weak transcription	Fetal Stomach	stomach
29	chr2:231226800-231231600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:231226800-231231600	Weak transcription	Ovary	ovary
31	chr2:231226800-231233800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr2:231226800-231233800	Weak transcription	Aorta	Aorta
33	chr2:231226800-231233800	Weak transcription	Spleen	Spleen
34	chr2:231226800-231235600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:231226800-231236400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:231226800-231237800	Weak transcription	Fetal Muscle Leg	muscle
37	chr2:231226800-231249800	Weak transcription	Lung	lung
38	chr2:231226800-231253600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:231226800-231253600	Weak transcription	Pancreas	Pancrea
40	chr2:231227000-231233600	Weak transcription	Fetal Thymus	thymus
41	chr2:231227000-231233800	Weak transcription	Left Ventricle	heart
42	chr2:231227000-231234600	Weak transcription	Placenta	Placenta
43	chr2:231227000-231235000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:231227000-231235200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:231227000-231235400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:231227000-231251400	Weak transcription	HSMMtube	muscle
47	chr2:231227200-231235600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:231227200-231242400	Weak transcription	HSMM	muscle
49	chr2:231227400-231231800	Weak transcription	GM12878-XiMat	blood
50	chr2:231227400-231232200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links