Variant report

Variant	rs7562674
Chromosome Location	chr2:172259687-172259688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172257799..172259945-chr2:172263821..172267063,3	K562	blood:
2	chr2:172015722..172018692-chr2:172257692..172260604,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198586	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1019363	0.81[EUR][1000 genomes]
rs10445762	0.90[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs10515933	0.89[ASW][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap]
rs17220419	0.89[ASW][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap]
rs17220734	0.89[ASW][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap]
rs17285541	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs17286415	0.89[ASW][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap]
rs17286660	0.81[YRI][hapmap]
rs2111718	0.81[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs2160849	0.81[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2356706	0.83[EUR][1000 genomes]
rs2356781	0.81[AFR][1000 genomes]
rs3731983	0.89[ASW][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap]
rs3795998	0.89[ASW][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap]
rs3821084	0.89[ASW][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap]
rs4458186	0.88[ASW][hapmap];0.84[LWK][hapmap]
rs4522571	0.89[ASW][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap]
rs4668382	0.81[EUR][1000 genomes]
rs4668386	0.83[AFR][1000 genomes]
rs4668387	0.89[ASW][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap]
rs62181337	0.81[EUR][1000 genomes]
rs62181338	0.81[EUR][1000 genomes]
rs62181339	0.81[EUR][1000 genomes]
rs62181340	0.83[EUR][1000 genomes]
rs62181342	0.89[EUR][1000 genomes]
rs62181352	0.87[AFR][1000 genomes]
rs62183468	0.83[AFR][1000 genomes]
rs62183539	0.83[AFR][1000 genomes]
rs6433290	0.87[AFR][1000 genomes]
rs6712315	0.88[EUR][1000 genomes]
rs7576894	0.85[YRI][hapmap];0.85[AFR][1000 genomes]
rs7595226	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7598137	0.89[ASW][hapmap];1.00[LWK][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes]
rs9678149	0.83[AFR][1000 genomes]
rs9679537	0.83[AFR][1000 genomes]
rs9789572	0.89[ASW][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap]
rs9789596	0.87[YRI][hapmap];0.83[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7562674	METTL8	cis	Esophagus Muscularis	GTEx
rs7562674	ATF2	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172222200-172289600	Weak transcription	Gastric	stomach
2	chr2:172238000-172272400	Weak transcription	Fetal Intestine Large	intestine
3	chr2:172238800-172272400	Weak transcription	Primary T cells from cord blood	blood
4	chr2:172248000-172266000	Weak transcription	Left Ventricle	heart
5	chr2:172248600-172265400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:172254600-172265400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:172256200-172260800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:172256200-172264000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr2:172256800-172263400	Weak transcription	Fetal Brain Male	brain
10	chr2:172257000-172261200	ZNF genes & repeats	GM12878-XiMat	blood
11	chr2:172257000-172266000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:172257600-172266000	Weak transcription	Aorta	Aorta
13	chr2:172257800-172259800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:172258000-172259800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:172258000-172262800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:172258200-172265200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:172258200-172265400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr2:172258600-172272400	Weak transcription	A549	lung
19	chr2:172259200-172261600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr2:172259200-172261600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:172259200-172261600	Enhancers	Osteobl	bone
22	chr2:172259200-172261800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:172259200-172261800	Enhancers	NH-A	brain
24	chr2:172259200-172262200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:172259400-172260000	Flanking Active TSS	HUVEC	blood vessel
26	chr2:172259400-172261800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:172259400-172261800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:172259400-172261800	Enhancers	HMEC	breast
29	chr2:172259400-172265400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:172259400-172272200	Weak transcription	Fetal Intestine Small	intestine
31	chr2:172259600-172259800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:172259600-172259800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:172259600-172259800	Enhancers	HSMMtube	muscle
34	chr2:172259600-172259800	Genic enhancers	NHDF-Ad	bronchial
35	chr2:172259600-172259800	Enhancers	NHLF	lung
36	chr2:172259600-172260000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:172259600-172260000	ZNF genes & repeats	K562	blood
38	chr2:172259600-172260200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:172259600-172260400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr2:172259600-172261000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:172259600-172261600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:172259600-172261800	Enhancers	HSMM	muscle
43	chr2:172259600-172262200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr2:172259600-172262200	Enhancers	Hela-S3	cervix
45	chr2:172259600-172262200	Enhancers	NHEK	skin

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