Variant report

Variant	rs55649340
Chromosome Location	chr6:80373585-80373586
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1033535	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12525799	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12526427	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs12526644	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12527512	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12527526	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12530052	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17505891	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883879	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34532743	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3812155	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3812159	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55781748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72901825	1.00[AFR][1000 genomes]
rs72905738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72905744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72905757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1018318	chr6:80241029-80465282	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80350600-80373600	Weak transcription	Gastric	stomach
2	chr6:80358400-80377800	Weak transcription	Spleen	Spleen
3	chr6:80359600-80376000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:80360000-80377800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:80360000-80378000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:80365000-80373600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:80365400-80378000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:80366200-80384000	Weak transcription	Brain Germinal Matrix	brain
9	chr6:80366400-80380600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:80372600-80373800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr6:80372600-80374400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr6:80372600-80374600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr6:80372600-80374600	Enhancers	Stomach Mucosa	stomach
14	chr6:80372600-80378800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr6:80372600-80382600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr6:80372800-80374000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:80372800-80374000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr6:80372800-80374400	Enhancers	Primary T cells fromperipheralblood	blood
19	chr6:80372800-80374400	Enhancers	K562	blood
20	chr6:80373000-80373800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:80373000-80374000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:80373000-80374200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:80373000-80374400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr6:80373000-80374400	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr6:80373000-80374400	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr6:80373000-80374400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr6:80373000-80374800	Strong transcription	Fetal Intestine Small	intestine
28	chr6:80373200-80373600	Active TSS	HepG2	liver
29	chr6:80373200-80374000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:80373200-80374200	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr6:80373200-80374400	Enhancers	Lung	lung
32	chr6:80373200-80374400	Enhancers	Pancreas	Pancrea
33	chr6:80373400-80373600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr6:80373400-80373800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:80373400-80373800	Enhancers	Esophagus	oesophagus
36	chr6:80373400-80373800	ZNF genes & repeats	Fetal Intestine Large	intestine
37	chr6:80373400-80374000	Enhancers	Left Ventricle	heart
38	chr6:80373400-80412400	Weak transcription	Fetal Brain Male	brain

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