Variant report

Variant	rs2252012
Chromosome Location	chr6:25313190-25313191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25298383..25300116-chr6:25311036..25313925,3	MCF-7	breast:
2	chr6:25307442..25309429-chr6:25310773..25313440,2	K562	blood:
3	chr6:25278102..25281759-chr6:25312379..25314512,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12055533	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12196702	0.83[ASN][1000 genomes]
rs1989206	0.98[ASN][1000 genomes]
rs2143022	0.91[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328878	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2690109	0.91[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2690115	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2690120	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690123	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690127	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2690129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690131	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2744290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2744296	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744299	0.92[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744302	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2744303	0.82[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4712908	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs9348670	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9356973	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9358850	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9358851	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9379751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9467465	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

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	esv16338	chr6:25312436-25315638	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25290400-25313400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:25301400-25313400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:25303200-25314800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:25303400-25315400	Weak transcription	Fetal Kidney	kidney
5	chr6:25305000-25324400	Weak transcription	Left Ventricle	heart
6	chr6:25306600-25331400	Weak transcription	Spleen	Spleen
7	chr6:25309200-25313400	Weak transcription	Ovary	ovary
8	chr6:25310200-25313600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:25310200-25313800	Enhancers	Fetal Intestine Large	intestine
10	chr6:25310200-25314200	Enhancers	Fetal Intestine Small	intestine
11	chr6:25310200-25316800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:25310400-25313800	Enhancers	Duodenum Mucosa	Duodenum
13	chr6:25310400-25319400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr6:25310800-25315000	Weak transcription	Brain Anterior Caudate	brain
15	chr6:25311200-25314000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:25311400-25313800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr6:25311400-25313800	Enhancers	Stomach Mucosa	stomach
18	chr6:25311400-25313800	Enhancers	HSMM	muscle
19	chr6:25311400-25314400	Enhancers	Osteobl	bone
20	chr6:25311600-25313200	Enhancers	HSMMtube	muscle
21	chr6:25311600-25313200	Enhancers	NHLF	lung
22	chr6:25311600-25313400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr6:25311600-25313800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr6:25311600-25313800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr6:25311600-25313800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:25311600-25313800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:25311600-25313800	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr6:25311600-25313800	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr6:25311600-25313800	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr6:25311600-25313800	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr6:25311600-25314000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr6:25311600-25314200	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr6:25311600-25314200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:25311600-25314400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr6:25311600-25315400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:25311600-25317200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:25311600-25317200	Enhancers	Fetal Lung	lung
38	chr6:25311800-25313200	Enhancers	Primary hematopoietic stem cells	blood
39	chr6:25311800-25313400	Enhancers	Primary T cells from cord blood	blood
40	chr6:25311800-25313800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr6:25311800-25313800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:25311800-25313800	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr6:25311800-25314000	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr6:25312000-25313400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:25312000-25313400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:25312000-25313400	Weak transcription	Lung	lung
47	chr6:25312000-25313600	Weak transcription	Placenta	Placenta
48	chr6:25312000-25314000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr6:25312000-25314200	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:25312000-25315600	Weak transcription	H9 Cell Line	embryonic stem cell

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