Variant report

Variant	rs6902583
Chromosome Location	chr6:28295533-28295534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr6:28293310-28295649	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28293963..28296628-chr6:28301528..28305497,4	MCF-7	breast:
2	chr6:28277054..28279277-chr6:28294657..28297286,2	K562	blood:

Variant related genes	Relation type
ZSCAN31	TF binding region
ENSG00000235109	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10080420	0.80[ASN][1000 genomes]
rs1150700	1.00[MEX][hapmap];0.92[YRI][hapmap]
rs1150715	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150722	0.86[ASW][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];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150723	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1150725	1.00[ASW][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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1225600	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332986	0.80[ASN][1000 genomes]
rs1600621	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679723	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1736892	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1778510	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108924	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2191036	0.80[ASN][1000 genomes]
rs2799076	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28475822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859375	1.00[JPT][hapmap]
rs3757180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3757183	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs6456812	1.00[ASW][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6456813	0.86[YRI][hapmap]
rs6456817	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6456820	0.80[ASN][1000 genomes]
rs6899512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6901001	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6908459	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6910120	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6912921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6918043	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6918631	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6922161	1.00[ASW][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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922302	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927023	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs6929449	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6929559	1.00[JPT][hapmap]
rs6938371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6941222	0.80[ASN][1000 genomes]
rs7747772	0.84[ASN][1000 genomes]
rs7752448	1.00[JPT][hapmap]
rs7752721	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs7759855	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7767897	1.00[ASW][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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295769	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs9295770	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9461450	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461452	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9468328	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468337	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468375	0.86[ASN][1000 genomes]
rs9468384	0.80[ASN][1000 genomes]
rs9654587	0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6902583	ZNF311	cis	lymphoblastoid	seeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28288200-28299200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:28290600-28295800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr6:28290800-28298200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr6:28291400-28295600	ZNF genes & repeats	Ovary	ovary
5	chr6:28291400-28298000	ZNF genes & repeats	Liver	Liver
6	chr6:28291600-28295600	ZNF genes & repeats	Psoas Muscle	Psoas
7	chr6:28291600-28295600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
8	chr6:28291600-28295600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
9	chr6:28291600-28296000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:28291800-28295600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
11	chr6:28292000-28295800	ZNF genes & repeats	Fetal Muscle Leg	muscle
12	chr6:28292600-28295600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
13	chr6:28292600-28295600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr6:28292600-28295600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
15	chr6:28292600-28297200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
16	chr6:28292800-28295600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
17	chr6:28292800-28295600	ZNF genes & repeats	Left Ventricle	heart
18	chr6:28292800-28295600	ZNF genes & repeats	Right Ventricle	heart
19	chr6:28292800-28295600	ZNF genes & repeats	HSMMtube	muscle
20	chr6:28292800-28295800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:28292800-28295800	ZNF genes & repeats	Adipose Nuclei	Adipose
22	chr6:28293000-28295600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr6:28293000-28295600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
24	chr6:28293200-28295600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:28293200-28295600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
26	chr6:28293200-28295600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:28293200-28295800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:28293400-28295600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
29	chr6:28293400-28295600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr6:28293400-28295600	ZNF genes & repeats	Colon Smooth Muscle	Colon
31	chr6:28293400-28295600	ZNF genes & repeats	Fetal Brain Female	brain
32	chr6:28293600-28295600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
33	chr6:28293600-28295600	ZNF genes & repeats	Brain Anterior Caudate	brain
34	chr6:28293600-28295600	ZNF genes & repeats	Brain Substantia Nigra	brain
35	chr6:28293600-28295600	ZNF genes & repeats	Colonic Mucosa	Colon
36	chr6:28293600-28295600	ZNF genes & repeats	Fetal Lung	lung
37	chr6:28293600-28295800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:28293600-28295800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
39	chr6:28293800-28295600	ZNF genes & repeats	Brain Germinal Matrix	brain
40	chr6:28293800-28295600	ZNF genes & repeats	Brain Hippocampus Middle	brain
41	chr6:28293800-28295600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:28293800-28295600	ZNF genes & repeats	Fetal Heart	heart
43	chr6:28293800-28295600	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr6:28293800-28295600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
45	chr6:28293800-28295600	ZNF genes & repeats	Spleen	Spleen
46	chr6:28293800-28295600	ZNF genes & repeats	K562	blood
47	chr6:28293800-28295800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:28293800-28295800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
49	chr6:28294000-28295600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
50	chr6:28294000-28295600	ZNF genes & repeats	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links