Variant report

Variant	rs2149226
Chromosome Location	chr6:25397449-25397450
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25366098..25368844-chr6:25396135..25397777,2	MCF-7	breast:
2	chr6:25387854..25389408-chr6:25395453..25397632,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10498723	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]
rs10498724	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]
rs10946767	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10946768	0.93[CHB][hapmap];0.94[JPT][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12524380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12525031	0.82[CHB][hapmap]
rs12529416	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16890520	0.85[YRI][hapmap]
rs16890531	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16890562	0.82[CHB][hapmap]
rs2149228	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]
rs2149229	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2182932	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2182933	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2328881	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2328882	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]
rs4711083	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4712924	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4712925	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4712926	0.93[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4712927	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4712928	0.82[CHB][hapmap]
rs4712930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4712931	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs55672111	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56248376	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72830734	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72830739	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72830741	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72830745	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72830747	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72830750	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72830753	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72830754	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs72830758	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72830759	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7751391	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]
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:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25377400-25410600	Weak transcription	Gastric	stomach
2	chr6:25383000-25403600	Weak transcription	Right Atrium	heart
3	chr6:25383600-25405000	Weak transcription	Fetal Intestine Small	intestine
4	chr6:25389400-25403600	Weak transcription	Thymus	Thymus
5	chr6:25390200-25399400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:25390200-25401800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:25390200-25405000	Weak transcription	Adipose Nuclei	Adipose
8	chr6:25390400-25401600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:25390400-25401600	Weak transcription	HMEC	breast
10	chr6:25390800-25399200	Weak transcription	Fetal Thymus	thymus
11	chr6:25391400-25403800	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr6:25392000-25398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:25394400-25403600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr6:25394600-25397600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:25395800-25397800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:25396000-25403600	Weak transcription	Primary T cells from cord blood	blood
17	chr6:25396200-25398000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr6:25396200-25403400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:25396600-25398800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:25397200-25397800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:25397200-25397800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr6:25397200-25397800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:25397200-25398000	Enhancers	H9 Cell Line	embryonic stem cell
24	chr6:25397200-25398000	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr6:25397200-25398000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr6:25397200-25398600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:25397400-25397600	Enhancers	Small Intestine	intestine
28	chr6:25397400-25397600	Enhancers	Stomach Mucosa	stomach
29	chr6:25397400-25397800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr6:25397400-25397800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:25397400-25397800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:25397400-25397800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:25397400-25398000	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr6:25397400-25398000	Enhancers	Aorta	Aorta
35	chr6:25397400-25398200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:25397400-25398400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:25397400-25399000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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