Variant report

Variant	rs3778077
Chromosome Location	chr6:34351767-34351768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34341570..34343991-chr6:34351093..34353761,2	K562	blood:
2	chr6:34339964..34342823-chr6:34350298..34352076,2	K562	blood:
3	chr6:34350156..34353339-chr6:34359370..34361777,7	MCF-7	breast:
4	chr6:34346665..34350255-chr6:34350707..34354463,4	MCF-7	breast:
5	chr6:34292790..34296171-chr6:34350622..34353853,3	K562	blood:

Variant related genes	Relation type
ENSG00000272325	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12662460	0.89[ASN][1000 genomes]
rs12664001	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12664016	0.80[ASN][1000 genomes]
rs12665397	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1573905	1.00[CEU][hapmap]
rs16885998	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16889706	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16889714	1.00[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs206919	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs206921	0.80[CHD][hapmap];0.86[JPT][hapmap]
rs206936	0.86[JPT][hapmap]
rs2071928	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28847046	0.85[ASN][1000 genomes]
rs34384951	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3798560	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs3798562	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3798564	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3800476	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3800477	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs414739	0.82[JPT][hapmap]
rs464553	0.82[JPT][hapmap]
rs4711390	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713766	1.00[CEU][hapmap]
rs4713770	0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4713772	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713773	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4713774	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713775	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713776	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713777	0.86[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4713780	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713781	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713783	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4713784	1.00[CEU][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes]
rs4713787	0.86[AMR][1000 genomes]
rs4713793	0.87[MEX][hapmap]
rs58648597	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59310759	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60100381	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61582147	0.81[AMR][1000 genomes]
rs62399909	0.84[ASN][1000 genomes]
rs6909732	1.00[CEU][hapmap]
rs6912971	0.82[JPT][hapmap]
rs6924682	0.83[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6925243	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs6935129	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7752035	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7767431	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7775635	0.85[ASN][1000 genomes]
rs9348940	0.82[AMR][1000 genomes]
rs9394200	1.00[CEU][hapmap]

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	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv1034978	chr6:34327526-34362187	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv981324	chr6:34351435-34360764	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3778077	RPS10	cis	lymphoblastoid	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34318200-34355800	Weak transcription	Brain Germinal Matrix	brain
2	chr6:34327800-34356400	Weak transcription	Hela-S3	cervix
3	chr6:34328600-34358000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:34331000-34358400	Weak transcription	Aorta	Aorta
5	chr6:34331400-34353400	Weak transcription	Small Intestine	intestine
6	chr6:34331400-34353600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:34331600-34353600	Weak transcription	Fetal Intestine Large	intestine
8	chr6:34333600-34358000	Weak transcription	HMEC	breast
9	chr6:34335200-34354600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:34335600-34358800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:34337800-34359000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:34338000-34353600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:34338200-34358600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr6:34338400-34353600	Weak transcription	Pancreas	Pancrea
15	chr6:34338400-34356600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:34338600-34351800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:34339200-34358000	Weak transcription	NHEK	skin
18	chr6:34339400-34358000	Weak transcription	HUVEC	blood vessel
19	chr6:34340400-34358000	Weak transcription	Fetal Thymus	thymus
20	chr6:34341000-34351800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr6:34342600-34355800	Weak transcription	Fetal Brain Female	brain
22	chr6:34342800-34353800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:34343000-34357600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:34343400-34356600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr6:34344000-34353800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:34345200-34358600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:34346600-34358400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:34346800-34353600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:34346800-34353600	Weak transcription	Spleen	Spleen
30	chr6:34346800-34353800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:34346800-34356400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr6:34347800-34351800	Weak transcription	Fetal Intestine Small	intestine
33	chr6:34349000-34358800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:34349200-34355000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:34350200-34353800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:34350400-34352200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:34350400-34352600	Enhancers	Fetal Kidney	kidney
38	chr6:34350400-34352800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:34350400-34354200	Enhancers	Lung	lung
40	chr6:34350600-34359000	Weak transcription	Esophagus	oesophagus
41	chr6:34350800-34352400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:34350800-34352800	Enhancers	Osteobl	bone
43	chr6:34351000-34351800	Genic enhancers	Primary B cells from cord blood	blood
44	chr6:34351000-34352200	Enhancers	Rectal Smooth Muscle	rectum
45	chr6:34351000-34352200	Enhancers	NHLF	lung
46	chr6:34351000-34352400	Enhancers	Brain Cingulate Gyrus	brain
47	chr6:34351000-34352400	Enhancers	Colon Smooth Muscle	Colon
48	chr6:34351000-34352800	Enhancers	Muscle Satellite Cultured Cells	--
49	chr6:34351000-34352800	Enhancers	Brain Anterior Caudate	brain
50	chr6:34351000-34352800	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links