Variant report

Variant	rs6452887
Chromosome Location	chr5:89790997-89790998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89790586..89793384-chr5:89813145..89814868,2	K562	blood:
2	chr5:89769093..89771320-chr5:89790048..89793265,3	MCF-7	breast:
3	chr5:89787239..89791726-chr5:89792887..89795524,4	K562	blood:
4	chr5:89780327..89783012-chr5:89790179..89792320,2	K562	blood:
5	chr5:89770745..89773686-chr5:89789440..89792433,3	K562	blood:

Variant related genes	Relation type
ENSG00000113356	Chromatin interaction
ENSG00000176055	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10056775	1.00[CEU][hapmap]
rs10514330	1.00[CEU][hapmap]
rs11742844	1.00[CEU][hapmap]
rs11745908	1.00[CEU][hapmap]
rs11748911	1.00[CEU][hapmap]
rs13159048	1.00[CEU][hapmap]
rs13169686	0.86[EUR][1000 genomes]
rs13182944	1.00[CEU][hapmap]
rs13186124	1.00[CEU][hapmap]
rs13189520	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13190272	1.00[CEU][hapmap]
rs1508788	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17541517	1.00[CEU][hapmap]
rs17541704	1.00[CEU][hapmap]
rs17541912	1.00[CEU][hapmap]
rs17542086	1.00[CEU][hapmap]
rs17542921	1.00[CEU][hapmap]
rs17543150	1.00[CEU][hapmap]
rs17614588	1.00[CEU][hapmap]
rs17621038	1.00[CEU][hapmap]
rs17621160	1.00[CEU][hapmap]
rs17621985	1.00[CEU][hapmap]
rs34685868	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35513125	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59607907	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6877613	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877977	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats 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	58 gene(s)	inside rSNPs	diseases
7	nsv882364	chr5:89748142-89808531	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 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	chr5:89771200-89796200	Weak transcription	Fetal Intestine Small	intestine
2	chr5:89771600-89798800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:89771600-89814400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:89773400-89795600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:89773600-89798800	Weak transcription	HMEC	breast
6	chr5:89773800-89816000	Weak transcription	HepG2	liver
7	chr5:89773800-89824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:89774000-89814600	Weak transcription	Dnd41	blood
9	chr5:89774400-89814600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:89776200-89799200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:89776200-89800400	Weak transcription	HUVEC	blood vessel
12	chr5:89776600-89798800	Weak transcription	NHEK	skin
13	chr5:89777000-89806600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:89780400-89799800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr5:89780400-89810800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:89780600-89822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:89780800-89800000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:89780800-89800400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:89781000-89799400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:89781200-89793600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:89783000-89800800	Weak transcription	A549	lung
22	chr5:89783800-89813400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:89784600-89795600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:89784800-89791000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:89784800-89814600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr5:89785200-89798800	Weak transcription	NHDF-Ad	bronchial
27	chr5:89785400-89798800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:89785400-89799400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr5:89785400-89814600	Weak transcription	NHLF	lung
30	chr5:89786200-89799400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:89788800-89799800	Weak transcription	NH-A	brain
32	chr5:89789800-89798200	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr5:89790000-89791000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr5:89790200-89794400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:89790200-89809600	Weak transcription	GM12878-XiMat	blood
36	chr5:89790400-89791000	Weak transcription	K562	blood
37	chr5:89790400-89792000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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