Variant report

Variant	rs2562520
Chromosome Location	chr5:89780945-89780946
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89780327..89783012-chr5:89790179..89792320,2	K562	blood:
2	chr5:89780920..89782434-chr5:89853716..89856481,2	MCF-7	breast:
3	chr5:89703597..89706583-chr5:89780566..89782809,3	K562	blood:
4	chr5:89776558..89779410-chr5:89779694..89781697,3	K562	blood:
5	chr5:89777835..89781277-chr5:89821033..89823702,3	K562	blood:
6	chr5:89769482..89772726-chr5:89779643..89782858,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164199	Chromatin interaction
ENSG00000153140	Chromatin interaction
ENSG00000113356	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000255647	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10942595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11750517	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs1544958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2115500	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2366768	0.91[JPT][hapmap]
rs250376	0.80[ASW][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.91[ASN][1000 genomes]
rs2562515	0.90[JPT][hapmap]
rs2562516	0.90[ASN][1000 genomes]
rs2562517	0.80[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2562518	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2562519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656953	0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs27658	0.91[JPT][hapmap]
rs2914672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2938788	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2963698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3805480	0.82[JPT][hapmap]
rs3933063	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6894539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7712322	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7722900	0.81[JPT][hapmap]
rs7726781	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv518131	chr5:89748142-89781594	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
8	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
9	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:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89771200-89784000	Weak transcription	Colon Smooth Muscle	Colon
2	chr5:89771200-89788600	Weak transcription	Psoas Muscle	Psoas
3	chr5:89771200-89796200	Weak transcription	Fetal Intestine Small	intestine
4	chr5:89771600-89798800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:89771600-89814400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr5:89772200-89784400	Weak transcription	Hela-S3	cervix
7	chr5:89772400-89784600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:89772600-89782200	Weak transcription	A549	lung
9	chr5:89773400-89795600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:89773600-89798800	Weak transcription	HMEC	breast
11	chr5:89773800-89816000	Weak transcription	HepG2	liver
12	chr5:89773800-89824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:89774000-89785800	Weak transcription	Adipose Nuclei	Adipose
14	chr5:89774000-89787600	Weak transcription	Brain Hippocampus Middle	brain
15	chr5:89774000-89814600	Weak transcription	Dnd41	blood
16	chr5:89774400-89781000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:89774400-89782000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:89774400-89814600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:89775000-89789800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:89775800-89784600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:89776200-89781000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:89776200-89789800	Weak transcription	GM12878-XiMat	blood
23	chr5:89776200-89799200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:89776200-89800400	Weak transcription	HUVEC	blood vessel
25	chr5:89776400-89784400	Weak transcription	NHDF-Ad	bronchial
26	chr5:89776600-89798800	Weak transcription	NHEK	skin
27	chr5:89776800-89784200	Weak transcription	Osteobl	bone
28	chr5:89776800-89784600	Weak transcription	NHLF	lung
29	chr5:89777000-89806600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:89779800-89781200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:89780200-89781000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
32	chr5:89780200-89781200	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:89780200-89782000	Strong transcription	K562	blood
34	chr5:89780400-89781200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:89780400-89782600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr5:89780400-89799800	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr5:89780400-89810800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:89780600-89781000	Enhancers	Fetal Heart	heart
39	chr5:89780600-89782600	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr5:89780600-89787600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr5:89780600-89822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr5:89780800-89782200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:89780800-89800000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr5:89780800-89800400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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