Variant report

Variant	rs6595837
Chromosome Location	chr5:127865360-127865361
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:127864261..127866407-chr5:127867220..127868792,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10039900	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10042096	0.95[ASN][1000 genomes]
rs10053025	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10062344	0.83[ASN][1000 genomes]
rs10063362	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10477685	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10478812	0.92[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs10478813	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10478814	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11960575	0.92[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs17164094	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17164113	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17164127	1.00[CHD][hapmap];0.81[JPT][hapmap]
rs17839642	0.92[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs1897998	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805652	0.94[CHD][hapmap];0.81[JPT][hapmap]
rs55721088	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55735252	0.83[ASN][1000 genomes]
rs56049336	0.91[ASN][1000 genomes]
rs57050667	0.95[ASN][1000 genomes]
rs58889726	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59674940	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60201468	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60571728	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60975118	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6595830	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6595831	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6595834	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6595836	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6860199	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6862508	0.81[JPT][hapmap]
rs6864057	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6868664	0.81[JPT][hapmap]
rs6881855	0.81[JPT][hapmap]
rs6886186	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6887851	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6892484	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6893116	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6893181	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6893248	0.83[ASN][1000 genomes]
rs6893301	0.83[ASN][1000 genomes]
rs73346331	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73784600	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73787623	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73787627	0.83[ASN][1000 genomes]
rs768744	0.82[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7703313	0.92[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs7708713	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7713044	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7722917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7722950	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7723500	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7725740	0.95[ASN][1000 genomes]
rs7726535	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9327478	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs981411	0.92[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv1015650	chr5:127745955-127866566	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
3	esv2763497	chr5:127745955-127882468	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv530822	chr5:127777365-127900742	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv427734	chr5:127805281-128088632	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1019560	chr5:127814656-127873680	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv537895	chr5:127814656-127873680	ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127827200-127870400	Weak transcription	Fetal Kidney	kidney
2	chr5:127840200-127870400	Weak transcription	Left Ventricle	heart
3	chr5:127840200-127872000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:127840400-127867600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:127841000-127870200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:127845600-127867800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:127845600-127870400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:127846000-127867800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:127847400-127869000	Weak transcription	NHDF-Ad	bronchial
10	chr5:127852800-127867800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:127853200-127872400	Weak transcription	Osteobl	bone
12	chr5:127853400-127867600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:127853600-127867800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:127854000-127872000	Weak transcription	Ovary	ovary
15	chr5:127855000-127867600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:127855000-127871200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:127855400-127867800	Weak transcription	Fetal Stomach	stomach
18	chr5:127857800-127869200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:127859400-127866600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:127860000-127868400	Genic enhancers	Fetal Heart	heart
21	chr5:127860200-127870400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr5:127861000-127870600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:127861000-127871000	Weak transcription	A549	lung
24	chr5:127861000-127871800	Weak transcription	Fetal Lung	lung
25	chr5:127861400-127867800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:127861800-127866400	Strong transcription	HMEC	breast
27	chr5:127861800-127869200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:127862400-127867400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr5:127862600-127872000	Weak transcription	NHLF	lung
30	chr5:127863200-127865800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:127863200-127872000	Weak transcription	HUVEC	blood vessel
32	chr5:127863600-127865400	Strong transcription	Fetal Muscle Leg	muscle
33	chr5:127863600-127867800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:127863600-127872000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:127863800-127866400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr5:127864000-127866000	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr5:127864000-127866200	Strong transcription	NHEK	skin
38	chr5:127864200-127867800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:127864600-127866200	Genic enhancers	Monocytes-CD14+_RO01746	blood
40	chr5:127864600-127871800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:127864800-127865400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:127864800-127867000	Strong transcription	Placenta	Placenta
43	chr5:127864800-127867200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr5:127864800-127867800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:127865000-127866400	Strong transcription	NH-A	brain
46	chr5:127865000-127867800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:127865200-127867200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:127865200-127868400	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links