Variant report

Variant	rs346486
Chromosome Location	chr4:86875667-86875668
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	chr4:86855497..86859080-chr4:86873833..86876584,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs189395	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs189396	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2043647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2136782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164538	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2575681	0.95[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2575682	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589505	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2589510	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2665869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2665876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346470	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346472	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346473	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346476	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs346477	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346483	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs346487	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346489	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346491	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346494	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346496	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346499	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs346500	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs346501	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62305515	0.89[ASN][1000 genomes]
rs62305516	0.89[ASN][1000 genomes]
rs62305518	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830000	chr4:86745341-86909059	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879520	chr4:86829529-86918232	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86854000-86893000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:86854200-86880200	Weak transcription	Gastric	stomach
3	chr4:86854200-86893000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:86854200-86915800	Weak transcription	Left Ventricle	heart
5	chr4:86858800-86876600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:86862400-86877200	Weak transcription	Liver	Liver
7	chr4:86863600-86902000	Weak transcription	Pancreas	Pancrea
8	chr4:86864000-86877000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr4:86873200-86875800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr4:86873200-86875800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr4:86873400-86875800	Enhancers	HSMM	muscle
12	chr4:86874000-86876400	Weak transcription	Fetal Kidney	kidney
13	chr4:86874200-86875800	Enhancers	Fetal Muscle Leg	muscle
14	chr4:86874400-86875800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:86874400-86876000	Enhancers	Hela-S3	cervix
16	chr4:86875000-86876200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:86875000-86876600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr4:86875000-86876600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:86875000-86877000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:86875000-86887200	Weak transcription	Fetal Stomach	stomach
21	chr4:86875000-86891200	Weak transcription	Right Atrium	heart
22	chr4:86875200-86876400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr4:86875200-86876400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr4:86875200-86876600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:86875200-86876800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr4:86875200-86876800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:86875200-86877600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:86875200-86877800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr4:86875200-86886800	Weak transcription	Adipose Nuclei	Adipose
30	chr4:86875200-86889000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:86875200-86889000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:86875200-86890800	Weak transcription	Stomach Mucosa	stomach
33	chr4:86875200-86915800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:86875400-86875800	Enhancers	A549	lung
35	chr4:86875400-86876400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr4:86875400-86876400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:86875400-86876400	Weak transcription	HUVEC	blood vessel
38	chr4:86875400-86876800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr4:86875400-86877000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr4:86875400-86877000	Weak transcription	HMEC	breast
41	chr4:86875400-86883200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:86875400-86888200	Weak transcription	HSMMtube	muscle
43	chr4:86875600-86876200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr4:86875600-86876400	Weak transcription	Primary B cells from cord blood	blood
45	chr4:86875600-86876600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr4:86875600-86876600	Weak transcription	NHDF-Ad	bronchial
47	chr4:86875600-86877000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:86875600-86882200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:86875600-86887400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links