Variant report

Variant	rs920560
Chromosome Location	chr4:102210349-102210350
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102206850..102209343-chr4:102209669..102211406,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1031033	0.81[ASN][1000 genomes]
rs1031034	0.81[ASN][1000 genomes]
rs1441433	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1561719	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2028475	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2099813	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2583400	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2583401	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2583402	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2583406	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2583410	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850332	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850339	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850344	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850348	0.98[EUR][1000 genomes]
rs2850349	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850350	0.99[EUR][1000 genomes]
rs2850351	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850352	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850354	0.97[EUR][1000 genomes]
rs2850355	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850356	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2850357	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850358	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850360	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2850366	0.81[ASN][1000 genomes]
rs2850368	0.81[ASN][1000 genomes]
rs2850954	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2850963	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850967	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850969	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850974	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850975	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2850976	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28664200	0.81[ASN][1000 genomes]
rs755961	0.94[EUR][1000 genomes]
rs920559	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs962384	0.95[EUR][1000 genomes];0.87[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	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
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102199600-102210400	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr4:102200000-102211800	Weak transcription	HMEC	breast
3	chr4:102200600-102211800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:102201000-102213000	Weak transcription	Fetal Heart	heart
5	chr4:102201200-102218200	Weak transcription	NHEK	skin
6	chr4:102201400-102214200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:102202200-102210600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:102204800-102211200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr4:102205000-102212600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:102205200-102210600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:102206600-102210600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr4:102206800-102210400	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr4:102207000-102216600	Weak transcription	NH-A	brain
14	chr4:102207200-102212000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:102207400-102212000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:102207400-102212000	Weak transcription	Gastric	stomach
17	chr4:102207400-102214200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:102207400-102214200	Weak transcription	Esophagus	oesophagus
19	chr4:102207600-102211400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:102207600-102226400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:102208000-102211200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:102208000-102212400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr4:102208200-102210600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:102208200-102210600	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr4:102208400-102210800	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr4:102208400-102211200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:102208600-102211200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr4:102208600-102212800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr4:102208600-102212800	Enhancers	Brain Anterior Caudate	brain
30	chr4:102208600-102213200	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr4:102208800-102210600	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr4:102208800-102210800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr4:102208800-102211800	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr4:102209000-102210400	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr4:102209000-102210400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:102209200-102210600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr4:102209200-102210600	Enhancers	Brain Substantia Nigra	brain
38	chr4:102209200-102210600	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr4:102209200-102211200	Enhancers	Primary B cells from cord blood	blood
40	chr4:102209400-102210600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:102209400-102211000	Weak transcription	Left Ventricle	heart
42	chr4:102209400-102211400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr4:102209400-102211800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr4:102209400-102211800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr4:102209400-102212000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:102209400-102212000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr4:102209400-102214200	Weak transcription	Aorta	Aorta
48	chr4:102209400-102214400	Weak transcription	Right Ventricle	heart
49	chr4:102209800-102210600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:102209800-102210600	Enhancers	NHDF-Ad	bronchial

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