Variant report

Variant	rs4582199
Chromosome Location	chr4:159053835-159053836
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:159050755..159053105-chr4:159053356..159055470,2	MCF-7	breast:
2	chr4:159031275..159033687-chr4:159053603..159055452,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10005007	0.93[ASN][1000 genomes]
rs10007737	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10008208	1.00[JPT][hapmap]
rs10012339	1.00[JPT][hapmap]
rs10016822	0.87[EUR][1000 genomes]
rs10018872	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10024133	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10026876	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10028490	1.00[JPT][hapmap]
rs10517689	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11100150	1.00[ASW][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11937022	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11938464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12502811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12511679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12645131	1.00[JPT][hapmap]
rs12648410	1.00[JPT][hapmap]
rs1320370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs14202	1.00[JPT][hapmap]
rs17036927	1.00[CEU][hapmap]
rs2346319	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346321	1.00[JPT][hapmap]
rs2346381	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2346774	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2346784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28499342	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28691778	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28719822	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2881373	1.00[JPT][hapmap]
rs2881473	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4234917	1.00[JPT][hapmap]
rs4317248	1.00[JPT][hapmap]
rs4324593	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4345228	1.00[JPT][hapmap]
rs4391084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4472184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4501266	0.86[ASW][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs4627913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4690893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691455	1.00[JPT][hapmap]
rs4691456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4691459	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691461	1.00[JPT][hapmap]
rs4691462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4691467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6536299	1.00[JPT][hapmap]
rs6812635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6813306	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6819576	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6820988	1.00[JPT][hapmap]
rs6821598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6830702	1.00[JPT][hapmap]
rs6832099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6833198	1.00[JPT][hapmap]
rs6834164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6849902	1.00[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6852646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7671094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7671501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7671934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7686997	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7695599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8180159	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8370	0.86[ASW][hapmap];1.00[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4582199	FLJ11155	cis	multi-tissue	Pritchard

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159042600-159060200	Weak transcription	Brain Substantia Nigra	brain
2	chr4:159042800-159054800	Weak transcription	Fetal Heart	heart
3	chr4:159042800-159083600	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:159044800-159071000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:159044800-159073200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:159045200-159058600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr4:159045200-159059400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr4:159046200-159054200	Strong transcription	HUVEC	blood vessel
9	chr4:159047000-159080200	Weak transcription	Right Ventricle	heart
10	chr4:159047200-159058600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:159049200-159070000	Weak transcription	Placenta	Placenta
12	chr4:159051000-159061000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:159051600-159056000	Weak transcription	Brain Hippocampus Middle	brain
14	chr4:159051800-159070600	Weak transcription	Fetal Intestine Large	intestine
15	chr4:159051800-159073000	Weak transcription	Fetal Stomach	stomach
16	chr4:159051800-159080400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:159052000-159054600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr4:159052000-159071400	Weak transcription	Adipose Nuclei	Adipose
19	chr4:159052200-159054000	Enhancers	NHDF-Ad	bronchial
20	chr4:159052200-159054200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:159052200-159055200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:159052200-159071400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:159052200-159072800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:159052400-159060200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:159052600-159060400	Weak transcription	Ovary	ovary
26	chr4:159052600-159071200	Weak transcription	Fetal Intestine Small	intestine
27	chr4:159052600-159071400	Weak transcription	HSMMtube	muscle
28	chr4:159052600-159080200	Weak transcription	Left Ventricle	heart
29	chr4:159052800-159060200	Weak transcription	HMEC	breast
30	chr4:159053000-159054400	Strong transcription	HSMM	muscle
31	chr4:159053400-159054200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr4:159053400-159054200	Enhancers	Aorta	Aorta
33	chr4:159053600-159054000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr4:159053800-159054000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:159053800-159054000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr4:159053800-159054000	Enhancers	Colon Smooth Muscle	Colon
37	chr4:159053800-159054000	Enhancers	HepG2	liver
38	chr4:159053800-159060600	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links