Variant report

Variant	rs820871
Chromosome Location	chr5:73980197-73980198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:73979598..73982392-chr5:73983812..73990818,9	MCF-7	breast:
2	chr5:73979909..73982593-chr5:73987219..73990536,5	MCF-7	breast:
3	chr5:72857771..72859719-chr5:73979974..73981658,2	K562	blood:
4	chr5:73980002..73981869-chr5:74633426..74635131,2	K562	blood:
5	chr5:73978938..73982006-chr5:74061565..74064417,3	K562	blood:
6	chr5:73979743..73983565-chr5:73984545..73990071,12	K562	blood:
7	chr5:73979647..73982006-chr5:74061742..74064417,2	K562	blood:

Variant related genes	Relation type
ENSG00000164331	Chromatin interaction
ENSG00000049860	Chromatin interaction
ENSG00000164346	Chromatin interaction
ENSG00000113161	Chromatin interaction
ENSG00000164347	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs6896615	0.83[AFR][1000 genomes]
rs820843	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs820864	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs820866	0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs820868	0.84[AFR][1000 genomes]
rs820869	0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs820870	0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs820872	0.81[YRI][hapmap];0.86[AFR][1000 genomes]
rs820879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820880	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820882	0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs820883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820886	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs820887	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs820888	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13844	chr5:73979961-73993853	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
2	nsv598652	chr5:73980182-73992881	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:73966800-73980200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:73966800-73980600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:73969800-73980600	Weak transcription	HMEC	breast
4	chr5:73969800-73980600	Weak transcription	HSMM	muscle
5	chr5:73969800-73980800	Weak transcription	NHLF	lung
6	chr5:73971800-73980200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:73973800-73980600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:73975200-73980200	Weak transcription	Spleen	Spleen
9	chr5:73976000-73980600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:73976200-73980200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr5:73976200-73980600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:73976200-73980600	Weak transcription	Osteobl	bone
13	chr5:73976200-73981000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:73976400-73980200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:73976400-73980200	Weak transcription	Hela-S3	cervix
16	chr5:73976800-73980600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:73977400-73980800	Weak transcription	HSMMtube	muscle
18	chr5:73978400-73980600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:73978400-73980600	Enhancers	Fetal Intestine Large	intestine
20	chr5:73978600-73980600	Enhancers	Fetal Intestine Small	intestine
21	chr5:73979000-73980200	Weak transcription	A549	lung
22	chr5:73979000-73980800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:73979000-73980800	Weak transcription	NH-A	brain
24	chr5:73979200-73980600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:73979200-73980600	Weak transcription	NHEK	skin
26	chr5:73979200-73980800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:73979400-73980600	Enhancers	Placenta	Placenta
28	chr5:73980000-73980400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:73980000-73980400	Bivalent Enhancer	HepG2	liver
30	chr5:73980000-73980400	Enhancers	K562	blood
31	chr5:73980000-73980600	Enhancers	Primary T cells fromperipheralblood	blood
32	chr5:73980000-73981600	Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links