Variant report

Variant	rs17370666
Chromosome Location	chr1:179841487-179841488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179839595..179843031-chr1:179844432..179847852,6	MCF-7	breast:
2	chr1:179841203..179843271-chr1:180138870..180141804,3	MCF-7	breast:
3	chr1:179838750..179842713-chr1:179849130..179852544,5	MCF-7	breast:
4	chr1:179840648..179843448-chr1:179843849..179845352,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272906	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000169905	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1148813	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1148814	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1148816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1148818	0.83[ASN][1000 genomes]
rs1281409	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1281414	0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1281415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1281419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1281424	0.83[ASN][1000 genomes]
rs1281425	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1281431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1290274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1295972	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1299683	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1299685	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1758143	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2281805	1.00[LWK][hapmap]
rs2762857	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2777907	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2777916	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2794584	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs476280	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs524166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs555755	0.94[EUR][1000 genomes]
rs576723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs627897	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs651455	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs668813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683812	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv519273	chr1:179831248-179847877	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179812600-179842600	Weak transcription	Stomach Mucosa	stomach
2	chr1:179820400-179841800	Weak transcription	Small Intestine	intestine
3	chr1:179820400-179844200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:179820400-179845400	Weak transcription	Right Ventricle	heart
5	chr1:179823800-179843200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:179826200-179843400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:179828000-179845600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:179829800-179844800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:179830200-179845200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:179830800-179842200	Strong transcription	K562	blood
11	chr1:179831200-179845000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:179832400-179844000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:179832400-179844200	Strong transcription	Fetal Thymus	thymus
14	chr1:179833200-179841800	Strong transcription	NH-A	brain
15	chr1:179834600-179844800	Weak transcription	Fetal Brain Male	brain
16	chr1:179834800-179844000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:179835000-179842600	Weak transcription	Fetal Kidney	kidney
18	chr1:179835000-179842800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:179835000-179843000	Weak transcription	Thymus	Thymus
20	chr1:179835000-179843200	Weak transcription	Pancreas	Pancrea
21	chr1:179835000-179843400	Weak transcription	Gastric	stomach
22	chr1:179835000-179844800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:179835000-179845600	Weak transcription	Ovary	ovary
24	chr1:179835000-179846400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:179835000-179846400	Weak transcription	Spleen	Spleen
26	chr1:179835200-179845000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:179835200-179845200	Weak transcription	Brain Angular Gyrus	brain
28	chr1:179835200-179845600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:179835400-179846000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:179836000-179841800	Weak transcription	Fetal Intestine Small	intestine
31	chr1:179836000-179843200	Weak transcription	Lung	lung
32	chr1:179836000-179844800	Weak transcription	HSMMtube	muscle
33	chr1:179836400-179841800	Weak transcription	Fetal Lung	lung
34	chr1:179836400-179842400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:179836400-179843400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:179836400-179844600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:179836600-179842200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:179836600-179842200	Weak transcription	Brain Anterior Caudate	brain
39	chr1:179836600-179842600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:179836600-179844200	Weak transcription	Esophagus	oesophagus
41	chr1:179836600-179845400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:179837000-179845600	Weak transcription	Aorta	Aorta
43	chr1:179837200-179843000	Weak transcription	Left Ventricle	heart
44	chr1:179837200-179845400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:179837400-179842400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:179837400-179843200	Weak transcription	Colonic Mucosa	Colon
47	chr1:179837400-179845000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr1:179837400-179845400	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:179837600-179845600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:179837800-179842400	Weak transcription	NHDF-Ad	bronchial

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