Variant report

Variant	rs479094
Chromosome Location	chr1:179842107-179842108
allele	A/G
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	chr1:179841843..179844701-chr1:179846021..179848651,3	MCF-7	breast:
3	chr1:179841983..179844053-chr1:180123561..180126113,2	K562	blood:
4	chr1:179841203..179843271-chr1:180138870..180141804,3	MCF-7	breast:
5	chr1:179838750..179842713-chr1:179849130..179852544,5	MCF-7	breast:
6	chr1:179840648..179843448-chr1:179843849..179845352,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116260	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000169905	Chromatin interaction
ENSG00000272906	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1014394	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs1144575	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1148812	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1148815	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1148817	0.88[EUR][1000 genomes]
rs12062341	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12062383	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1281378	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1281408	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1281411	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1281412	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1281413	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1281428	0.94[ASN][1000 genomes]
rs1281429	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1281430	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1281432	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1298477	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1298479	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1300068	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2007148	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245425	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2249346	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2762858	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2777908	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2777909	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2777917	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2794582	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2794583	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs474258	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs475233	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs475434	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480377	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480498	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs486906	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs501300	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs502036	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs505789	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs505837	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs507603	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs514421	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs518774	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs522534	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs530369	0.81[CEU][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs530854	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs531814	0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs538512	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs547776	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs549650	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs553830	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs555270	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs555526	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs589780	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs599185	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs600046	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs600553	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs605807	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609521	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs612215	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs615337	0.80[EUR][1000 genomes]
rs644412	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7530362	0.82[EUR][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	chr1:179820400-179844200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:179820400-179845400	Weak transcription	Right Ventricle	heart
4	chr1:179823800-179843200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:179826200-179843400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:179828000-179845600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:179829800-179844800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:179830200-179845200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:179830800-179842200	Strong transcription	K562	blood
10	chr1:179831200-179845000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:179832400-179844000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:179832400-179844200	Strong transcription	Fetal Thymus	thymus
13	chr1:179834600-179844800	Weak transcription	Fetal Brain Male	brain
14	chr1:179834800-179844000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:179835000-179842600	Weak transcription	Fetal Kidney	kidney
16	chr1:179835000-179842800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:179835000-179843000	Weak transcription	Thymus	Thymus
18	chr1:179835000-179843200	Weak transcription	Pancreas	Pancrea
19	chr1:179835000-179843400	Weak transcription	Gastric	stomach
20	chr1:179835000-179844800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:179835000-179845600	Weak transcription	Ovary	ovary
22	chr1:179835000-179846400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:179835000-179846400	Weak transcription	Spleen	Spleen
24	chr1:179835200-179845000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:179835200-179845200	Weak transcription	Brain Angular Gyrus	brain
26	chr1:179835200-179845600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:179835400-179846000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:179836000-179843200	Weak transcription	Lung	lung
29	chr1:179836000-179844800	Weak transcription	HSMMtube	muscle
30	chr1:179836400-179842400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:179836400-179843400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:179836400-179844600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:179836600-179842200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:179836600-179842200	Weak transcription	Brain Anterior Caudate	brain
35	chr1:179836600-179842600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:179836600-179844200	Weak transcription	Esophagus	oesophagus
37	chr1:179836600-179845400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:179837000-179845600	Weak transcription	Aorta	Aorta
39	chr1:179837200-179843000	Weak transcription	Left Ventricle	heart
40	chr1:179837200-179845400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:179837400-179842400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:179837400-179843200	Weak transcription	Colonic Mucosa	Colon
43	chr1:179837400-179845000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:179837400-179845400	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:179837600-179845600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr1:179837800-179842400	Weak transcription	NHDF-Ad	bronchial
47	chr1:179837800-179842800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:179837800-179842800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:179837800-179843400	Weak transcription	NHLF	lung
50	chr1:179838000-179842400	Weak transcription	Primary hematopoietic stem cells	blood

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