Variant report

Variant	rs6724428
Chromosome Location	chr2:189377509-189377510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:188707921..188708505-chr2:189376811..189377638,2	MCF-7	breast:
2	chr2:188458841..188460185-chr2:189376734..189377597,3	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10804020	0.86[ASW][hapmap];0.81[CEU][hapmap]
rs10931359	0.86[ASW][hapmap];0.81[CEU][hapmap]
rs11685321	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465164	0.81[CEU][hapmap]
rs12465625	0.81[CEU][hapmap]
rs12473872	0.82[CEU][hapmap];0.85[YRI][hapmap]
rs12474692	0.82[CEU][hapmap]
rs13005128	1.00[ASN][1000 genomes]
rs13008931	0.81[CEU][hapmap]
rs1354906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1605462	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4396679	1.00[JPT][hapmap]
rs4516391	0.81[CEU][hapmap]
rs7422239	0.85[ASN][1000 genomes]
rs7566619	0.87[ASW][hapmap];0.81[CEU][hapmap]
rs7586390	0.87[ASW][hapmap];0.81[CEU][hapmap]

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	nsv584055	chr2:189266823-189493686	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv834489	chr2:189329027-189494224	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1003974	chr2:189331760-189827814	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv533110	chr2:189354436-189462552	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189329200-189399000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:189344200-189390400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:189355800-189382400	Weak transcription	Gastric	stomach
4	chr2:189359200-189382200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:189361800-189392000	Weak transcription	Ovary	ovary
6	chr2:189362800-189382200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:189367800-189382800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:189370400-189379400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:189371800-189380200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:189371800-189382200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:189371800-189394000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:189372000-189380200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:189372000-189380800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:189372200-189382200	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:189374400-189380000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:189376200-189378800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:189376200-189380800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:189376400-189382200	Weak transcription	Aorta	Aorta
19	chr2:189376800-189377600	Enhancers	Fetal Kidney	kidney
20	chr2:189377000-189387400	Weak transcription	Fetal Lung	lung
21	chr2:189377200-189377600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:189377400-189377800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:189377400-189377800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:189377400-189377800	Enhancers	Muscle Satellite Cultured Cells	--
25	chr2:189377400-189383000	Weak transcription	HUVEC	blood vessel

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