Variant report

Variant	rs12504870
Chromosome Location	chr4:48257008-48257009
allele	C/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:48255521..48259627-chr4:48261501..48267509,10	K562	blood:
2	chr4:48250701..48254731-chr4:48255352..48259390,5	K562	blood:
3	chr4:48255711..48257883-chr4:48270489..48272038,2	MCF-7	breast:
4	chr4:48175041..48176757-chr4:48255815..48257585,2	K562	blood:
5	chr4:48255487..48257034-chr4:48270351..48271892,2	K562	blood:
6	chr4:48256167..48259627-chr4:48260322..48264297,6	K562	blood:
7	chr4:48248411..48250691-chr4:48255149..48257827,3	K562	blood:
8	chr4:48255045..48260439-chr4:48268334..48274456,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000135605	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10454242	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs12500187	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes]
rs12507853	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13103259	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13104355	0.85[EUR][1000 genomes]
rs13114469	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs13120599	0.85[EUR][1000 genomes]
rs13121247	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13125176	0.83[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1355218	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471308	0.85[EUR][1000 genomes]
rs17471321	0.85[EUR][1000 genomes]
rs17574806	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17574819	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17574847	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352597	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457412	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2664021	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs2664030	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704391	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704394	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704403	0.85[EUR][1000 genomes]
rs2704404	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs2704412	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34292660	0.85[EUR][1000 genomes]
rs34712902	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35602964	0.84[AFR][1000 genomes]
rs35912788	0.85[EUR][1000 genomes]
rs35920857	0.85[EUR][1000 genomes]
rs36103122	0.85[EUR][1000 genomes]
rs4694891	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55657817	0.85[EUR][1000 genomes]
rs60092950	0.83[EUR][1000 genomes]
rs6826144	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs6850058	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs73246007	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73817608	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7658983	0.85[EUR][1000 genomes]
rs7659013	0.85[EUR][1000 genomes]
rs7663382	0.85[EUR][1000 genomes]
rs7669018	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678247	0.84[EUR][1000 genomes]
rs7678843	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs7698045	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9996158	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2763359	chr4:48189710-48290233	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
4	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv461357	chr4:48248258-48274152	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv594119	chr4:48248258-48274152	Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
8	nsv470032	chr4:48251915-48312389	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv461358	chr4:48251916-48274152	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
10	nsv594120	chr4:48251916-48274152	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
11	nsv4329	chr4:48254113-48262973	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48248800-48270600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:48249600-48261600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr4:48250600-48259400	Weak transcription	Small Intestine	intestine
4	chr4:48251400-48270000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:48251800-48270200	Weak transcription	Fetal Intestine Large	intestine
6	chr4:48252600-48258200	Enhancers	Fetal Heart	heart
7	chr4:48253000-48263000	Weak transcription	Primary B cells from cord blood	blood
8	chr4:48253200-48257400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:48254800-48257600	Weak transcription	NHEK	skin
10	chr4:48254800-48257800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr4:48255200-48258000	Enhancers	Fetal Lung	lung
12	chr4:48255400-48257400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:48255400-48257400	Enhancers	Brain Germinal Matrix	brain
14	chr4:48255600-48257400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:48255600-48257800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:48255800-48257200	Enhancers	NHLF	lung
17	chr4:48255800-48257400	Enhancers	NHDF-Ad	bronchial
18	chr4:48255800-48258400	Enhancers	Left Ventricle	heart
19	chr4:48256000-48257200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:48256000-48257800	Enhancers	Liver	Liver
21	chr4:48256200-48257400	Enhancers	Esophagus	oesophagus
22	chr4:48256200-48257400	Enhancers	Right Ventricle	heart
23	chr4:48256200-48257600	Enhancers	Gastric	stomach
24	chr4:48256200-48258200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr4:48256200-48258200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:48256200-48258400	Enhancers	Lung	lung
27	chr4:48256600-48258000	Flanking Active TSS	K562	blood
28	chr4:48256800-48257400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:48256800-48257400	Strong transcription	GM12878-XiMat	blood
30	chr4:48256800-48257600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:48256800-48257600	Enhancers	Stomach Mucosa	stomach
32	chr4:48256800-48258400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:48256800-48264800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:48257000-48257800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:48257000-48257800	Enhancers	Duodenum Mucosa	Duodenum
36	chr4:48257000-48258800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:48257000-48263600	Weak transcription	HSMM	muscle

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