Variant report

Variant	rs3798560
Chromosome Location	chr6:34343566-34343567
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:34337455..34341004-chr6:34341961..34344805,4	K562	blood:
2	chr6:34343338..34346512-chr6:34355803..34358188,3	K562	blood:
3	chr6:34342154..34345431-chr6:34346779..34350168,4	K562	blood:
4	chr6:34342605..34345308-chr6:34346623..34348686,2	MCF-7	breast:
5	chr6:34342189..34346729-chr6:34358969..34361667,6	K562	blood:
6	chr6:34341570..34343991-chr6:34351093..34353761,2	K562	blood:
7	chr6:34335584..34339226-chr6:34339692..34345370,5	K562	blood:
8	chr6:34342887..34344725-chr6:34348668..34351040,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272325	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs12664016	0.83[AFR][1000 genomes]
rs16885998	0.85[CHD][hapmap]
rs16889706	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs169584	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1811968	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2006833	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs206919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs206920	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs206921	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs206924	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs206925	0.83[EUR][1000 genomes]
rs206936	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs206941	0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs206942	0.94[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2237098	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28847046	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3778077	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs3798556	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3798562	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs3913009	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3913010	0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs410340	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs414739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs458576	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4587164	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs464553	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4711390	0.89[CHD][hapmap];0.82[JPT][hapmap]
rs4713770	0.83[CHB][hapmap]
rs4713774	0.82[JPT][hapmap]
rs4713777	0.88[CHD][hapmap];0.82[JPT][hapmap]
rs568502	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57622072	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs611928	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs62399909	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6457773	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6907486	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6912971	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6924482	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6924682	0.95[CHD][hapmap];0.86[JPT][hapmap]
rs6924982	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6925243	0.94[ASW][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.89[MKK][hapmap];0.93[YRI][hapmap]
rs6930978	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7752035	0.86[JPT][hapmap]
rs7757586	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7757900	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7765498	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7773447	0.80[EUR][1000 genomes]
rs7775635	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9366856	0.83[EUR][1000 genomes]
rs9368810	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9368813	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9380433	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9380435	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9394214	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9394215	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9394218	0.83[EUR][1000 genomes]
rs9461981	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9469775	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9469779	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9469780	0.82[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3798560	NUDT3	Cis_1M	lymphoblastoid	RTeQTL
rs3798560	RPS10	cis	lymphoblastoid	seeQTL
rs3798560	RPS10	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 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	chr6:34331200-34344400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:34331200-34346000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:34331200-34346200	Weak transcription	Brain Substantia Nigra	brain
17	chr6:34331200-34346200	Weak transcription	Stomach Mucosa	stomach
18	chr6:34331200-34351600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr6:34331400-34345800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:34331400-34346000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:34331400-34348600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:34331400-34351400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr6:34331400-34353400	Weak transcription	Small Intestine	intestine
24	chr6:34331400-34353600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:34331600-34351400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:34331600-34353600	Weak transcription	Fetal Intestine Large	intestine
27	chr6:34332000-34345600	Weak transcription	Primary T cells from cord blood	blood
28	chr6:34333600-34358000	Weak transcription	HMEC	breast
29	chr6:34334200-34350400	Weak transcription	Lung	lung
30	chr6:34334600-34345800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:34334600-34348600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:34334600-34350400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:34334800-34345600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr6:34334800-34345800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:34334800-34346400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:34335200-34354600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:34335600-34358800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:34337800-34359000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:34338000-34353600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:34338200-34346400	Weak transcription	A549	lung
41	chr6:34338200-34350000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:34338200-34351600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:34338200-34358600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:34338400-34345600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:34338400-34346000	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr6:34338400-34346000	Weak transcription	HSMM	muscle
47	chr6:34338400-34351000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:34338400-34353600	Weak transcription	Pancreas	Pancrea
49	chr6:34338400-34356600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr6:34338600-34348200	Weak transcription	Dnd41	blood

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