Variant report

Variant	rs7575189
Chromosome Location	chr2:174015168-174015169
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	chr2:173912619..173914756-chr2:174014173..174017350,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091428	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11680612	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs13004345	1.00[ASW][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.98[MKK][hapmap];0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13009008	0.87[ASN][1000 genomes]
rs13030866	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17760899	0.80[CEU][hapmap]
rs1837470	0.91[ASW][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs35109796	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs35339538	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3754745	0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs3754747	0.84[LWK][hapmap]
rs3769184	0.82[ASW][hapmap];0.83[CHB][hapmap];0.89[LWK][hapmap];0.92[MKK][hapmap];0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3769185	0.89[CEU][hapmap];0.83[CHB][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4344898	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4972397	0.88[CEU][hapmap];0.82[CHB][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6722254	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6758859	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs6759787	0.81[CEU][hapmap]
rs734993	0.84[LWK][hapmap]
rs9636294	0.81[CEU][hapmap];0.87[TSI][hapmap]

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	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv834461	chr2:173979734-174038471	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7575189	SCRN3	cis	parietal	SCAN
rs7575189	METTL8	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174007800-174021000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:174007800-174021000	Weak transcription	Fetal Intestine Small	intestine
3	chr2:174008600-174020800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:174012600-174015400	Enhancers	A549	lung
5	chr2:174012800-174015200	Enhancers	Fetal Heart	heart
6	chr2:174012800-174015800	Enhancers	Left Ventricle	heart
7	chr2:174012800-174016000	Enhancers	NHEK	skin
8	chr2:174012800-174016200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:174012800-174016600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:174012800-174018000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:174012800-174018400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:174012800-174018400	Enhancers	HMEC	breast
13	chr2:174012800-174018400	Enhancers	Osteobl	bone
14	chr2:174012800-174018600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:174012800-174018600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:174012800-174018600	Enhancers	NHDF-Ad	bronchial
17	chr2:174012800-174018600	Enhancers	NHLF	lung
18	chr2:174012800-174020000	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr2:174012800-174026600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr2:174013000-174016000	Weak transcription	Small Intestine	intestine
21	chr2:174013000-174017600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:174013000-174018000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:174013200-174016000	Enhancers	Right Atrium	heart
24	chr2:174013200-174016400	Enhancers	Psoas Muscle	Psoas
25	chr2:174013200-174017200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:174013200-174018600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:174013400-174025400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:174013600-174015800	Weak transcription	Right Ventricle	heart
29	chr2:174013600-174015800	Weak transcription	HUVEC	blood vessel
30	chr2:174013600-174016400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr2:174013600-174017200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:174013600-174018000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:174013600-174024600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:174013800-174015200	Weak transcription	NH-A	brain
35	chr2:174014200-174015600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:174014400-174015400	Enhancers	Adipose Nuclei	Adipose
37	chr2:174014400-174017200	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr2:174014400-174017400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:174014400-174017400	Enhancers	HSMM	muscle
40	chr2:174014400-174018400	Enhancers	Hela-S3	cervix
41	chr2:174014600-174015200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr2:174014600-174015200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:174014600-174015200	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr2:174014600-174015200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr2:174014600-174015200	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr2:174014600-174015200	Enhancers	Colon Smooth Muscle	Colon
47	chr2:174014600-174015600	Enhancers	HSMMtube	muscle
48	chr2:174014600-174016400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:174014600-174016800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:174014600-174018200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links