Variant report

Variant	rs2063058
Chromosome Location	chr4:102076982-102076983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102075628..102078181-chr4:102267682..102270641,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254531	Chromatin interaction
ENSG00000138814	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10018021	0.81[EUR][1000 genomes]
rs10030389	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs10516471	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs13103902	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13111186	0.82[EUR][1000 genomes]
rs13112866	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs13118966	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs13125501	0.81[EUR][1000 genomes]
rs13128841	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13135924	0.82[EUR][1000 genomes]
rs13142024	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs1810024	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1880943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2659552	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695215	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695217	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695219	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3811063	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs4590038	0.82[EUR][1000 genomes]
rs4698912	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4698913	0.82[EUR][1000 genomes]
rs4699106	0.82[EUR][1000 genomes]
rs7677550	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs950177	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs9995338	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102062600-102090400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:102068800-102077400	Weak transcription	Small Intestine	intestine
3	chr4:102069000-102078600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:102070000-102077000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr4:102070000-102078400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:102070600-102078200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:102072400-102077400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:102074200-102078600	Enhancers	Brain Anterior Caudate	brain
9	chr4:102074200-102080800	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr4:102074600-102080600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:102074800-102077600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr4:102075000-102077200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:102075000-102078600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:102075000-102079600	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr4:102075200-102077800	Weak transcription	Brain Angular Gyrus	brain
16	chr4:102075200-102080600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr4:102075400-102078200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:102075400-102078400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:102075400-102084200	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr4:102075600-102078200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:102075800-102077400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:102075800-102077400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr4:102075800-102077800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr4:102075800-102078400	Weak transcription	Primary B cells from cord blood	blood
25	chr4:102075800-102078800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:102076200-102077000	Enhancers	A549	lung
27	chr4:102076200-102078600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:102076200-102078800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:102076200-102078800	Enhancers	HMEC	breast
30	chr4:102076200-102079600	Enhancers	NHEK	skin
31	chr4:102076200-102079800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr4:102076400-102077200	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr4:102076400-102077200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:102076400-102077200	Enhancers	Hela-S3	cervix
35	chr4:102076400-102077400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:102076400-102077600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:102076400-102077600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:102076400-102077600	Enhancers	Brain Substantia Nigra	brain
39	chr4:102076400-102077800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:102076400-102077800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:102076400-102078000	Enhancers	Osteobl	bone
42	chr4:102076400-102078400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr4:102076400-102079400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:102076400-102079400	Enhancers	NHDF-Ad	bronchial
45	chr4:102076400-102080000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:102076400-102080000	Enhancers	NH-A	brain
47	chr4:102076400-102080400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr4:102076400-102080600	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr4:102076400-102080600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:102076400-102080600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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