Variant report

Variant	rs62368280
Chromosome Location	chr5:50012323-50012324
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	chr5:49961597..49964689-chr5:50010010..50013411,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151883	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12656200	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12658769	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13158037	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13168120	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13170746	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16884728	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34776244	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35940648	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56187641	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62365520	0.88[EUR][1000 genomes]
rs62366935	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62366936	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62368283	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71615982	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7700817	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7719213	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7723602	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv818352	chr5:49958221-50017724	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv537759	chr5:49986171-50033616	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv1030068	chr5:49986171-50047352	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv537760	chr5:49986171-50047352	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv1016237	chr5:49986171-50118816	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv537761	chr5:49986171-50118816	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
17	nsv521214	chr5:49988020-50037381	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv462160	chr5:49988020-50058043	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	nsv598109	chr5:49988020-50058043	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	nsv598110	chr5:49988020-50089919	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
21	nsv462162	chr5:49989701-50040778	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	nsv598111	chr5:49989701-50040778	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv598112	chr5:49989701-50062611	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
24	nsv462163	chr5:49989701-50088317	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
25	nsv598113	chr5:49989701-50088317	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
26	nsv598114	chr5:49991561-50088317	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50006200-50013600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:50007200-50016000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:50007200-50020200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:50007400-50016000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:50007400-50016200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:50007400-50017200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:50007400-50022400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:50007400-50022400	Weak transcription	Gastric	stomach
9	chr5:50007600-50012400	Weak transcription	Small Intestine	intestine
10	chr5:50007600-50012800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:50007600-50017200	Weak transcription	NHEK	skin
12	chr5:50007600-50020200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr5:50007800-50012600	Enhancers	Primary T cells from cord blood	blood
14	chr5:50007800-50014000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr5:50007800-50017800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr5:50007800-50020000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr5:50007800-50031000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr5:50008200-50013000	Weak transcription	Liver	Liver
19	chr5:50008400-50016600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr5:50008800-50012400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr5:50008800-50017200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr5:50009000-50016600	Weak transcription	Dnd41	blood
23	chr5:50009200-50023200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr5:50009400-50015400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:50009400-50016000	Weak transcription	Fetal Thymus	thymus
26	chr5:50009400-50016200	Weak transcription	Esophagus	oesophagus
27	chr5:50009600-50012800	Weak transcription	Primary B cells from cord blood	blood
28	chr5:50009800-50013000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr5:50010200-50018200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr5:50010800-50013400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr5:50010800-50015800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr5:50010800-50016000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr5:50010800-50016000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:50011000-50013400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:50011000-50016000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:50011000-50016000	Weak transcription	Fetal Lung	lung
37	chr5:50011000-50016600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:50011000-50020200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:50011200-50013000	Weak transcription	GM12878-XiMat	blood
40	chr5:50011200-50015600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:50011200-50015800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:50011200-50016000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:50011400-50016000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr5:50011400-50016000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr5:50011400-50022400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:50011800-50014800	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr5:50011800-50014800	Enhancers	Duodenum Mucosa	Duodenum
48	chr5:50011800-50015200	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr5:50012000-50012600	Enhancers	Stomach Mucosa	stomach
50	chr5:50012000-50013000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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