Variant report

Variant	rs639216
Chromosome Location	chr1:120217414-120217415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:120216915..120218562-chr1:120252926..120255494,2	MCF-7	breast:
2	chr1:120207222..120209789-chr1:120216328..120218570,3	K562	blood:
3	chr1:120204131..120206731-chr1:120214943..120217556,2	MCF-7	breast:
4	chr1:120207377..120209340-chr1:120217218..120219975,2	MCF-7	breast:
5	chr1:120215638..120218365-chr1:120219886..120221935,2	K562	blood:
6	chr1:120216865..120219033-chr1:120220435..120223044,2	K562	blood:
7	chr1:120189265..120193710-chr1:120213010..120218911,11	MCF-7	breast:
8	chr1:120217105..120219498-chr1:120262347..120264026,2	MCF-7	breast:
9	chr1:120189180..120192171-chr1:120215646..120218336,2	K562	blood:
10	chr1:120154003..120154965-chr1:120217033..120218809,10	K562	blood:
11	chr1:120156126..120157196-chr1:120217116..120218704,11	MCF-7	breast:
12	chr1:120215935..120218673-chr1:120225082..120226675,2	MCF-7	breast:
13	chr1:120202631..120203644-chr1:120217187..120218365,3	K562	blood:
14	chr1:120216390..120222237-chr1:120252306..120257638,5	MCF-7	breast:
15	chr1:120155133..120157085-chr1:120217009..120218744,10	K562	blood:
16	chr1:120216874..120219563-chr1:120253751..120255810,3	K562	blood:
17	chr1:120189291..120191976-chr1:120215677..120217877,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143067	Chromatin interaction
ENSG00000092621	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1163251	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2764886	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs477992	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs478093	0.88[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs478450	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs483180	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs483360	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs487081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493427	0.86[CEU][hapmap]
rs496195	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs496198	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514491	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs517533	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs532303	0.89[ASN][1000 genomes]
rs539708	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541503	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs561931	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs592762	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs594400	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs595283	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs597308	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs598685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs606312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611365	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs612430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs627707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629735	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs639761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640195	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658442	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs660073	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs662243	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs662602	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs666930	0.85[CHD][hapmap]
rs677277	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs839600	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs839605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839607	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs839608	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs866321	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120203800-120217800	Weak transcription	Fetal Stomach	stomach
2	chr1:120210200-120218000	Weak transcription	GM12878-XiMat	blood
3	chr1:120212800-120218000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:120214800-120218000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr1:120215000-120217800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:120215200-120217600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr1:120215200-120218000	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:120215200-120219000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:120215200-120219600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:120215400-120217800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr1:120215400-120217800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:120215400-120218000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:120215800-120218000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr1:120216000-120217600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr1:120216000-120217600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:120216000-120217600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:120216000-120218000	Enhancers	HSMMtube	muscle
18	chr1:120216000-120218000	Enhancers	NH-A	brain
19	chr1:120216200-120217800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:120216200-120218000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:120216200-120218600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:120216400-120217800	Enhancers	Liver	Liver
23	chr1:120216400-120218000	Weak transcription	Fetal Intestine Small	intestine
24	chr1:120216400-120218000	Enhancers	NHDF-Ad	bronchial
25	chr1:120216600-120217600	Flanking Active TSS	Osteobl	bone
26	chr1:120216600-120217800	Enhancers	Fetal Heart	heart
27	chr1:120216600-120217800	Enhancers	Fetal Lung	lung
28	chr1:120216600-120218000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:120216600-120218000	Enhancers	HSMM	muscle
30	chr1:120216600-120218000	Enhancers	K562	blood
31	chr1:120216600-120218400	Flanking Active TSS	NHEK	skin
32	chr1:120216600-120218600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr1:120216600-120218800	Flanking Active TSS	HUVEC	blood vessel
34	chr1:120216800-120217600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:120216800-120217800	Weak transcription	Placenta	Placenta
36	chr1:120216800-120218000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:120216800-120218200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:120217000-120218000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:120217000-120218000	Flanking Active TSS	HepG2	liver
40	chr1:120217200-120217600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr1:120217200-120217800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:120217200-120217800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:120217200-120217800	Weak transcription	Fetal Kidney	kidney
44	chr1:120217200-120218000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr1:120217200-120218000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:120217200-120218000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:120217200-120218000	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr1:120217200-120218600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:120217200-120218800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:120217200-120219000	Enhancers	Hela-S3	cervix

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