Variant report

Variant	rs2690125
Chromosome Location	chr6:25302617-25302618
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25277631..25279275-chr6:25301822..25304144,2	MCF-7	breast:
2	chr6:25302209..25304566-chr6:25321319..25323421,2	MCF-7	breast:
3	chr6:25279234..25282196-chr6:25302311..25304060,2	K562	blood:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 30 )
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];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12196702	0.81[ASN][1000 genomes]
rs1989206	0.96[ASN][1000 genomes]
rs2143022	0.92[CEU][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2252012	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]
rs2328878	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690109	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2690115	0.84[ASN][1000 genomes]
rs2690120	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2690123	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2690127	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2690129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2690131	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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];0.97[ASN][1000 genomes]
rs2744296	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2744299	0.92[CEU][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2744302	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2744303	0.82[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4712908	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9348670	0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9356973	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9358850	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9358851	0.82[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9379751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467465	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

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:91 , 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	chr6:25297200-25303200	Weak transcription	Primary T cells from cord blood	blood
6	chr6:25297400-25303000	Weak transcription	Gastric	stomach
7	chr6:25297400-25304600	Weak transcription	Left Ventricle	heart
8	chr6:25298000-25302800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:25298000-25302800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:25298000-25303200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:25298000-25311800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:25298200-25303000	Weak transcription	Fetal Kidney	kidney
13	chr6:25298600-25303000	Enhancers	Aorta	Aorta
14	chr6:25298600-25303400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:25299000-25302800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:25300600-25302800	Enhancers	Duodenum Mucosa	Duodenum
17	chr6:25300600-25303200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr6:25300600-25303600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr6:25300600-25304000	Enhancers	Primary B cells from peripheral blood	blood
20	chr6:25300800-25302800	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr6:25300800-25303000	Enhancers	Small Intestine	intestine
22	chr6:25300800-25303400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr6:25300800-25304000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr6:25301000-25303000	Enhancers	Adipose Nuclei	Adipose
25	chr6:25301000-25304000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:25301200-25303000	Enhancers	Fetal Lung	lung
27	chr6:25301200-25303200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr6:25301200-25303800	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr6:25301200-25303800	Enhancers	Primary hematopoietic stem cells	blood
30	chr6:25301200-25305400	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr6:25301400-25302800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:25301400-25302800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:25301400-25302800	Weak transcription	Pancreas	Pancrea
34	chr6:25301400-25303400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr6:25301400-25303800	Enhancers	Primary B cells from cord blood	blood
36	chr6:25301400-25313400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:25301600-25302800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr6:25301600-25303400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:25301600-25304200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:25301600-25311600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr6:25301800-25302800	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr6:25301800-25302800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:25301800-25304200	Enhancers	NHLF	lung
44	chr6:25301800-25305600	Enhancers	Fetal Intestine Large	intestine
45	chr6:25301800-25306000	Enhancers	Fetal Intestine Small	intestine
46	chr6:25302000-25302800	Weak transcription	Fetal Muscle Leg	muscle
47	chr6:25302000-25303000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:25302000-25303000	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr6:25302000-25303000	Enhancers	NHDF-Ad	bronchial
50	chr6:25302000-25303200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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