Variant report

Variant	rs3798562
Chromosome Location	chr6:34344578-34344579
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:34344409..34346828-chr6:34354344..34357154,2	K562	blood:
2	chr6:34337455..34341004-chr6:34341961..34344805,4	K562	blood:
3	chr6:34343338..34346512-chr6:34355803..34358188,3	K562	blood:
4	chr6:34342154..34345431-chr6:34346779..34350168,4	K562	blood:
5	chr6:34342605..34345308-chr6:34346623..34348686,2	MCF-7	breast:
6	chr6:34344455..34346805-chr6:34358307..34361667,3	K562	blood:
7	chr6:34342189..34346729-chr6:34358969..34361667,6	K562	blood:
8	chr6:34215453..34218624-chr6:34344414..34346174,3	K562	blood:
9	chr6:34335584..34339226-chr6:34339692..34345370,5	K562	blood:
10	chr6:34342887..34344725-chr6:34348668..34351040,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272325	Chromatin interaction
ENSG00000186577	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12662460	0.89[ASN][1000 genomes]
rs12664001	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12665397	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1573905	1.00[CEU][hapmap]
rs16885998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16889706	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16889714	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs206919	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs206921	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs206936	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs206942	0.80[CHD][hapmap]
rs2071928	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28847046	0.82[ASN][1000 genomes]
rs34384951	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3778077	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]
rs3798560	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs3798564	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3800476	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3800477	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs414739	0.82[JPT][hapmap]
rs464553	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs4711390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713766	1.00[CEU][hapmap]
rs4713770	0.82[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4713772	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713773	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713775	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4713776	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713777	0.87[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4713780	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713781	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4713783	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4713784	1.00[CEU][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs4713787	0.86[AMR][1000 genomes]
rs4713793	0.83[MEX][hapmap]
rs58648597	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59310759	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60100381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs611928	0.82[CHD][hapmap]
rs61582147	0.81[AMR][1000 genomes]
rs62399909	0.86[ASN][1000 genomes]
rs6909732	1.00[CEU][hapmap]
rs6912971	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs6924682	0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6925243	0.83[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs6930978	0.82[CHD][hapmap]
rs6935129	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7752035	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7767431	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7775635	0.82[ASN][1000 genomes]
rs9348940	0.82[AMR][1000 genomes]
rs9394200	1.00[CEU][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3798562	RPS10	cis	lymphoblastoid	seeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34309800-34347200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:34315400-34351200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:34318200-34355800	Weak transcription	Brain Germinal Matrix	brain
4	chr6:34320400-34350400	Weak transcription	Esophagus	oesophagus
5	chr6:34327000-34351600	Weak transcription	Ovary	ovary
6	chr6:34327800-34356400	Weak transcription	Hela-S3	cervix
7	chr6:34328000-34345400	Weak transcription	Fetal Stomach	stomach
8	chr6:34328000-34351200	Weak transcription	Gastric	stomach
9	chr6:34328600-34358000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:34329600-34345800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:34329800-34346400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:34329800-34351200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:34331000-34358400	Weak transcription	Aorta	Aorta
14	chr6:34331200-34346000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:34331200-34346200	Weak transcription	Brain Substantia Nigra	brain
16	chr6:34331200-34346200	Weak transcription	Stomach Mucosa	stomach
17	chr6:34331200-34351600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:34331400-34345800	Weak transcription	Fetal Intestine Small	intestine
19	chr6:34331400-34346000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:34331400-34348600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:34331400-34351400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:34331400-34353400	Weak transcription	Small Intestine	intestine
23	chr6:34331400-34353600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr6:34331600-34351400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:34331600-34353600	Weak transcription	Fetal Intestine Large	intestine
26	chr6:34332000-34345600	Weak transcription	Primary T cells from cord blood	blood
27	chr6:34333600-34358000	Weak transcription	HMEC	breast
28	chr6:34334200-34350400	Weak transcription	Lung	lung
29	chr6:34334600-34345800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:34334600-34348600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:34334600-34350400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:34334800-34345600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr6:34334800-34345800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:34334800-34346400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:34335200-34354600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:34335600-34358800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:34337800-34359000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:34338000-34353600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr6:34338200-34346400	Weak transcription	A549	lung
40	chr6:34338200-34350000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:34338200-34351600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:34338200-34358600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:34338400-34345600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:34338400-34346000	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr6:34338400-34346000	Weak transcription	HSMM	muscle
46	chr6:34338400-34351000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:34338400-34353600	Weak transcription	Pancreas	Pancrea
48	chr6:34338400-34356600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr6:34338600-34348200	Weak transcription	Dnd41	blood
50	chr6:34338600-34351200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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