Variant report

Variant	rs1879659
Chromosome Location	chr4:159044250-159044251
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:159042649..159044924-chr4:159061563..159064027,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10008208	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10012339	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10018872	1.00[JPT][hapmap]
rs10024133	1.00[JPT][hapmap]
rs10028490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10517689	1.00[JPT][hapmap]
rs11100151	1.00[JPT][hapmap]
rs11731973	0.83[CEU][hapmap]
rs11938464	1.00[JPT][hapmap]
rs12502811	1.00[JPT][hapmap]
rs12511679	1.00[JPT][hapmap]
rs12645131	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12648410	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1320370	1.00[JPT][hapmap]
rs1320371	1.00[JPT][hapmap]
rs14202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346320	1.00[JPT][hapmap]
rs2346321	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2346381	1.00[JPT][hapmap]
rs2346776	1.00[JPT][hapmap]
rs2346780	1.00[JPT][hapmap]
rs2346781	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346784	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2881373	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4234917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4309890	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4317248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4345228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4389619	0.93[CEU][hapmap]
rs4391084	1.00[JPT][hapmap]
rs4472184	1.00[JPT][hapmap]
rs4501266	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4582199	1.00[JPT][hapmap]
rs4627913	1.00[JPT][hapmap]
rs4690893	1.00[JPT][hapmap]
rs4691455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691456	1.00[JPT][hapmap]
rs4691457	1.00[JPT][hapmap]
rs4691458	1.00[JPT][hapmap]
rs4691461	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691462	1.00[JPT][hapmap]
rs4691463	1.00[JPT][hapmap]
rs4691464	1.00[JPT][hapmap]
rs4691465	1.00[JPT][hapmap]
rs4691467	1.00[JPT][hapmap]
rs6536299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6812635	1.00[JPT][hapmap]
rs6820988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6821598	1.00[JPT][hapmap]
rs6830702	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6832099	1.00[JPT][hapmap]
rs6833198	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6834164	1.00[JPT][hapmap]
rs6849902	1.00[JPT][hapmap]
rs6852646	1.00[JPT][hapmap]
rs6852878	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6855420	1.00[JPT][hapmap]
rs7671094	1.00[JPT][hapmap]
rs7671501	1.00[JPT][hapmap]
rs7671934	1.00[JPT][hapmap]
rs7695599	1.00[JPT][hapmap]
rs8370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv880293	chr4:159012365-159049020	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1879659	RP11-597D13.9	cis	Skin Sun Exposed Lower leg	GTEx
rs1879659	TMEM144	cis	Nerve Tibial	GTEx
rs1879659	TMEM144	cis	Esophagus Muscularis	GTEx
rs1879659	RP11-597D13.9	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159034200-159046200	Weak transcription	HUVEC	blood vessel
2	chr4:159041400-159044600	Enhancers	HSMM	muscle
3	chr4:159042000-159044400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:159042000-159046800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:159042200-159048000	Weak transcription	Fetal Intestine Large	intestine
6	chr4:159042200-159051400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:159042400-159044600	Enhancers	NHDF-Ad	bronchial
8	chr4:159042400-159050800	Weak transcription	Aorta	Aorta
9	chr4:159042600-159044400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:159042600-159044600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:159042600-159053400	Weak transcription	Right Atrium	heart
12	chr4:159042600-159053600	Weak transcription	Brain Anterior Caudate	brain
13	chr4:159042600-159060200	Weak transcription	Brain Substantia Nigra	brain
14	chr4:159042800-159044400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:159042800-159044600	Enhancers	Colon Smooth Muscle	Colon
16	chr4:159042800-159044600	Enhancers	HSMMtube	muscle
17	chr4:159042800-159046400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:159042800-159046400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:159042800-159046400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:159042800-159047000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:159042800-159047200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:159042800-159047200	Weak transcription	Adipose Nuclei	Adipose
23	chr4:159042800-159047400	Weak transcription	HMEC	breast
24	chr4:159042800-159048000	Weak transcription	HepG2	liver
25	chr4:159042800-159049000	Weak transcription	Ovary	ovary
26	chr4:159042800-159050000	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:159042800-159053400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr4:159042800-159053800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr4:159042800-159054800	Weak transcription	Fetal Heart	heart
30	chr4:159042800-159083600	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:159043000-159044800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:159043200-159051200	Weak transcription	Left Ventricle	heart
33	chr4:159043400-159044400	Enhancers	Rectal Smooth Muscle	rectum
34	chr4:159043800-159044600	Enhancers	NHLF	lung
35	chr4:159043800-159045200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr4:159043800-159045200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr4:159043800-159051400	Weak transcription	Fetal Stomach	stomach
38	chr4:159044000-159045800	Weak transcription	NH-A	brain
39	chr4:159044000-159048000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:159044000-159049800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr4:159044200-159044600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:159044200-159046800	Weak transcription	Fetal Kidney	kidney
43	chr4:159044200-159052200	Weak transcription	Osteobl	bone

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