Variant report

Variant	rs3769185
Chromosome Location	chr2:174013499-174013500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:174011042..174014620-chr2:174016771..174020819,3	MCF-7	breast:
2	chr2:174001713..174004612-chr2:174011601..174013779,2	K562	blood:
3	chr2:173944994..173946697-chr2:174012717..174014873,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11680612	0.95[ASN][1000 genomes]
rs11901217	0.81[EUR][1000 genomes]
rs13004345	0.80[ASW][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.90[ASN][1000 genomes]
rs13009008	0.84[ASN][1000 genomes]
rs13030866	0.90[ASN][1000 genomes]
rs1837470	0.81[ASW][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.92[MKK][hapmap];0.95[ASN][1000 genomes]
rs35109796	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35339538	0.90[ASN][1000 genomes]
rs3769184	0.91[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.95[ASN][1000 genomes]
rs4344898	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4972534	0.91[ASN][1000 genomes]
rs6722254	0.98[ASN][1000 genomes]
rs6746656	0.81[TSI][hapmap]
rs6750801	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7575189	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]
rs8446	0.88[JPT][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3769185	METTL8	cis	parietal	SCAN
rs3769185	ZAK	Cis_1M	lymphoblastoid	RTeQTL
rs3769185	SCRN3	cis	parietal	SCAN
rs3769185	BBS5	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174002200-174014600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:174002200-174014600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:174006600-174014400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr2:174007800-174021000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:174007800-174021000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:174008000-174013600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:174008600-174020800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:174012600-174015400	Enhancers	A549	lung
9	chr2:174012800-174013600	Enhancers	Right Ventricle	heart
10	chr2:174012800-174013800	Enhancers	Colon Smooth Muscle	Colon
11	chr2:174012800-174013800	Enhancers	NH-A	brain
12	chr2:174012800-174014600	Enhancers	Ovary	ovary
13	chr2:174012800-174015200	Enhancers	Fetal Heart	heart
14	chr2:174012800-174015800	Enhancers	Left Ventricle	heart
15	chr2:174012800-174016000	Enhancers	NHEK	skin
16	chr2:174012800-174016200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:174012800-174016600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:174012800-174018000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr2:174012800-174018400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:174012800-174018400	Enhancers	HMEC	breast
21	chr2:174012800-174018400	Enhancers	Osteobl	bone
22	chr2:174012800-174018600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:174012800-174018600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:174012800-174018600	Enhancers	NHDF-Ad	bronchial
25	chr2:174012800-174018600	Enhancers	NHLF	lung
26	chr2:174012800-174020000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:174012800-174026600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr2:174013000-174013800	Enhancers	Rectal Smooth Muscle	rectum
29	chr2:174013000-174014600	Enhancers	Stomach Smooth Muscle	stomach
30	chr2:174013000-174016000	Weak transcription	Small Intestine	intestine
31	chr2:174013000-174017600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:174013000-174018000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:174013200-174013600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr2:174013200-174013600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:174013200-174013600	Enhancers	HUVEC	blood vessel
36	chr2:174013200-174013800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:174013200-174014400	Enhancers	GM12878-XiMat	blood
38	chr2:174013200-174014400	Weak transcription	HSMM	muscle
39	chr2:174013200-174016000	Enhancers	Right Atrium	heart
40	chr2:174013200-174016400	Enhancers	Psoas Muscle	Psoas
41	chr2:174013200-174017200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:174013200-174018600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:174013400-174013600	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr2:174013400-174025400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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