Variant report

Variant	rs1880271
Chromosome Location	chr6:25301406-25301407
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	chr6:25290098..25292506-chr6:25299738..25301945,2	MCF-7	breast:
2	chr6:25278449..25281272-chr6:25299737..25301781,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1046141	1.00[CHD][hapmap]
rs11759648	1.00[CHD][hapmap]
rs1900552	1.00[CHD][hapmap]
rs2044553	1.00[CHD][hapmap]
rs2690047	1.00[CHD][hapmap]
rs2690076	1.00[CHD][hapmap]
rs2690102	1.00[CHD][hapmap]
rs2690116	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2690119	0.85[AFR][1000 genomes]
rs2690122	0.98[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2690124	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744282	1.00[CHD][hapmap]
rs2744292	0.83[YRI][hapmap];0.88[AFR][1000 genomes]
rs2744295	0.92[AFR][1000 genomes]
rs6456653	1.00[CHD][hapmap]
rs7739830	1.00[CHD][hapmap]
rs7755584	1.00[CHD][hapmap]
rs940405	1.00[CHD][hapmap]
rs9467496	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25280800-25302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:25290400-25313400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:25292200-25303000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr6:25294200-25311200	Weak transcription	Lung	lung
5	chr6:25294600-25301600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:25296400-25302400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:25296600-25302400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:25296600-25302600	Weak transcription	Colonic Mucosa	Colon
9	chr6:25296800-25301800	Weak transcription	Fetal Intestine Large	intestine
10	chr6:25296800-25302200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:25297200-25302600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:25297200-25303200	Weak transcription	Primary T cells from cord blood	blood
13	chr6:25297400-25301600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:25297400-25301800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:25297400-25302400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:25297400-25303000	Weak transcription	Gastric	stomach
17	chr6:25297400-25304600	Weak transcription	Left Ventricle	heart
18	chr6:25297600-25301800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:25297800-25302400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:25298000-25301800	Weak transcription	Stomach Mucosa	stomach
21	chr6:25298000-25302400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:25298000-25302400	Weak transcription	Ovary	ovary
23	chr6:25298000-25302800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:25298000-25302800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr6:25298000-25303200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:25298000-25311800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr6:25298200-25303000	Weak transcription	Fetal Kidney	kidney
28	chr6:25298400-25302600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:25298600-25303000	Enhancers	Aorta	Aorta
30	chr6:25298600-25303400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr6:25298800-25302000	Weak transcription	Fetal Heart	heart
32	chr6:25298800-25302600	Weak transcription	HSMMtube	muscle
33	chr6:25299000-25301800	Weak transcription	NHLF	lung
34	chr6:25299000-25302600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:25299000-25302800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:25299200-25302400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr6:25300600-25302800	Enhancers	Duodenum Mucosa	Duodenum
38	chr6:25300600-25303200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr6:25300600-25303600	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr6:25300600-25304000	Enhancers	Primary B cells from peripheral blood	blood
41	chr6:25300800-25301600	Enhancers	H1 Cell Line	embryonic stem cell
42	chr6:25300800-25302000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:25300800-25302200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr6:25300800-25302800	Enhancers	Rectal Mucosa Donor 29	rectum
45	chr6:25300800-25303000	Enhancers	Small Intestine	intestine
46	chr6:25300800-25303400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr6:25300800-25304000	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr6:25301000-25301600	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr6:25301000-25301800	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr6:25301000-25301800	Enhancers	Duodenum Smooth Muscle	Duodenum

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