Variant report

Variant	rs3769179
Chromosome Location	chr2:174036608-174036609
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:174034052..174036635-chr2:174040991..174043810,2	MCF-7	breast:
2	chr2:174024599..174026346-chr2:174036575..174038101,2	K562	blood:
3	chr2:174027701..174029324-chr2:174034830..174037383,2	K562	blood:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11901996	1.00[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs12996371	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs16861266	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs16861279	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs16861295	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16861304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16861323	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2053964	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2119123	0.85[JPT][hapmap]
rs2119124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2289395	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs3769155	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.84[MEX][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3769164	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs3769166	0.88[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3769175	0.81[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3769176	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.96[ASN][1000 genomes]
rs3769183	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs3769206	0.82[CHB][hapmap]
rs4632313	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs58407376	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59935415	0.96[ASN][1000 genomes]
rs61183795	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6433398	0.85[CEU][hapmap]
rs6717067	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6725795	1.00[CEU][hapmap]
rs6753354	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73971702	0.96[ASN][1000 genomes]
rs7566222	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs7571788	0.96[ASN][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	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

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174015400-174047000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:174016200-174048800	Weak transcription	K562	blood
3	chr2:174024800-174037200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:174026000-174036800	Weak transcription	Small Intestine	intestine
5	chr2:174026000-174037400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:174026000-174037800	Weak transcription	Aorta	Aorta
7	chr2:174026000-174069000	Weak transcription	Primary B cells from cord blood	blood
8	chr2:174026200-174036800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:174026200-174040600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:174026200-174045000	Weak transcription	Fetal Intestine Small	intestine
11	chr2:174026400-174039600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr2:174026400-174047600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:174026600-174037800	Weak transcription	Right Ventricle	heart
14	chr2:174026600-174048800	Weak transcription	Liver	Liver
15	chr2:174026600-174083200	Weak transcription	Esophagus	oesophagus
16	chr2:174028200-174044200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:174028400-174054600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:174030000-174037600	Weak transcription	Left Ventricle	heart
19	chr2:174030000-174052200	Weak transcription	Fetal Lung	lung
20	chr2:174030800-174036800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:174030800-174037600	Weak transcription	Psoas Muscle	Psoas
22	chr2:174030800-174037800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:174031000-174036800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:174031000-174036800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:174031200-174046600	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:174032400-174048800	Weak transcription	Dnd41	blood
27	chr2:174032600-174036800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:174032600-174036800	Weak transcription	Hela-S3	cervix
29	chr2:174035000-174037600	Enhancers	A549	lung
30	chr2:174035200-174037000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr2:174035600-174037400	Enhancers	Fetal Heart	heart
32	chr2:174035800-174036800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:174035800-174037400	Enhancers	NHLF	lung
34	chr2:174035800-174037600	Enhancers	NHDF-Ad	bronchial
35	chr2:174035800-174038400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr2:174036000-174037400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:174036000-174037400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:174036000-174037600	Enhancers	Osteobl	bone
39	chr2:174036400-174037400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:174036600-174037000	Enhancers	Adipose Nuclei	Adipose
41	chr2:174036600-174037200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:174036600-174037400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:174036600-174037400	Enhancers	NHEK	skin

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