Variant report

Variant	rs820885
Chromosome Location	chr5:73983049-73983050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:73969331..73972056-chr5:73981357..73983781,2	MCF-7	breast:
2	chr5:73981038..73983852-chr5:73999852..74002635,2	MCF-7	breast:
3	chr5:73981324..73983563-chr5:74077397..74079724,2	K562	blood:
4	chr5:73981661..73984902-chr5:74226605..74228461,3	K562	blood:
5	chr5:73980953..73983731-chr5:74012002..74014571,3	MCF-7	breast:
6	chr5:73983027..73985005-chr5:74061405..74062936,2	K562	blood:
7	chr5:73979743..73983565-chr5:73984545..73990071,12	K562	blood:

Variant related genes	Relation type
ENSG00000049860	Chromatin interaction
ENSG00000164347	Chromatin interaction
ENSG00000164346	Chromatin interaction
ENSG00000239517	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12519436	0.89[MKK][hapmap]
rs2936918	0.82[AFR][1000 genomes]
rs3756443	0.85[MKK][hapmap]
rs6896615	0.85[AFR][1000 genomes]
rs820843	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs820864	0.83[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs820866	0.94[ASW][hapmap];0.87[LWK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs820867	0.81[AFR][1000 genomes]
rs820868	0.85[AFR][1000 genomes]
rs820869	0.94[ASW][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs820870	0.94[ASW][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs820871	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]
rs820872	0.94[ASW][hapmap];0.89[LWK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs820879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820880	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820881	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820882	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs820883	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820884	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs820886	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs820887	0.96[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:4 , 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
3	nsv934214	chr5:73981349-73993050	Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv933165	chr5:73981599-73993050	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs820885	HEXB	cis	lymphoblastoid	seeQTL
rs820885	HEXB	cis	cerebellum	SCAN
rs820885	ZNF366	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:73981400-73983200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr5:73981400-73983200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr5:73981400-73983200	Flanking Active TSS	Dnd41	blood
4	chr5:73981600-73983400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:73981600-73983400	Flanking Active TSS	Brain Anterior Caudate	brain
6	chr5:73981600-73983400	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr5:73981600-73983400	Flanking Active TSS	Hela-S3	cervix
8	chr5:73981800-73983200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:73981800-73983200	Enhancers	Spleen	Spleen
10	chr5:73981800-73983400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:73981800-73983400	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr5:73981800-73983400	Flanking Active TSS	NHLF	lung
13	chr5:73982000-73983200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:73982000-73983200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:73982000-73983200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:73982000-73983200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr5:73982000-73983200	Enhancers	Small Intestine	intestine
18	chr5:73982000-73983200	Flanking Active TSS	GM12878-XiMat	blood
19	chr5:73982000-73983200	Flanking Active TSS	NHDF-Ad	bronchial
20	chr5:73982000-73983400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:73982000-73983400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr5:73982000-73983400	Enhancers	Right Atrium	heart
23	chr5:73982000-73983400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr5:73982000-73988800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:73982000-73989000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr5:73982000-73994400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr5:73982000-74002200	Weak transcription	Fetal Brain Female	brain
28	chr5:73982000-74017400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr5:73982000-74061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:73982200-73983200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr5:73982200-73983200	Enhancers	Aorta	Aorta
32	chr5:73982200-73983200	Enhancers	Esophagus	oesophagus
33	chr5:73982200-73983200	Enhancers	A549	lung
34	chr5:73982200-73983200	Flanking Active TSS	HepG2	liver
35	chr5:73982200-73983200	Transcr. at gene 5' and 3'	NHEK	skin
36	chr5:73982200-73983400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr5:73982200-73983400	Enhancers	Liver	Liver
38	chr5:73982200-73983400	Enhancers	Psoas Muscle	Psoas
39	chr5:73982200-73983400	Enhancers	Stomach Mucosa	stomach
40	chr5:73982200-73984600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:73982200-73985000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:73982200-73985200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:73982200-73987200	Weak transcription	Fetal Lung	lung
44	chr5:73982200-74020600	Weak transcription	Fetal Brain Male	brain
45	chr5:73982400-73983200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:73982400-73983200	Enhancers	Primary T cells fromperipheralblood	blood
47	chr5:73982400-73983200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr5:73982400-73983200	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr5:73982400-73983400	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr5:73982400-73983400	Enhancers	Primary B cells from cord blood	blood

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