Variant report

Variant	rs2328882
Chromosome Location	chr6:25395277-25395278
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	chr6:25394649..25396533-chr6:25398062..25399864,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10498723	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]
rs10498724	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]
rs10946767	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10946768	0.93[CHB][hapmap];0.94[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12524380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525031	0.82[CHB][hapmap]
rs12529416	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16890520	0.85[YRI][hapmap]
rs16890531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16890562	0.82[CHB][hapmap]
rs2149226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2149228	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]
rs2149229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711083	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712917	0.80[JPT][hapmap]
rs4712924	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4712925	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4712926	0.93[CHB][hapmap];0.89[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4712927	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712928	0.82[CHB][hapmap]
rs4712930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4712931	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs55672111	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56248376	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72830734	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72830739	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72830741	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72830745	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72830747	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72830750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72830753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72830754	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72830758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72830759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7751391	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]
rs7769124	0.85[YRI][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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830612	chr6:25342408-25509758	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25377400-25410600	Weak transcription	Gastric	stomach
2	chr6:25377800-25395600	Weak transcription	Pancreas	Pancrea
3	chr6:25383000-25403600	Weak transcription	Right Atrium	heart
4	chr6:25383600-25405000	Weak transcription	Fetal Intestine Small	intestine
5	chr6:25388400-25395800	Weak transcription	Primary T cells from cord blood	blood
6	chr6:25388400-25396000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:25388400-25396000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:25389400-25397400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:25389400-25403600	Weak transcription	Thymus	Thymus
10	chr6:25390200-25397400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:25390200-25399400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:25390200-25401800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:25390200-25405000	Weak transcription	Adipose Nuclei	Adipose
14	chr6:25390400-25401600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:25390400-25401600	Weak transcription	HMEC	breast
16	chr6:25390800-25397400	Weak transcription	Aorta	Aorta
17	chr6:25390800-25399200	Weak transcription	Fetal Thymus	thymus
18	chr6:25391400-25403800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:25392000-25398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:25393000-25397200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:25393400-25397200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:25393400-25397400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:25393400-25397400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:25394400-25395800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:25394400-25403600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr6:25394600-25397400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:25394600-25397600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:25394800-25395400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:25395200-25395400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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