Variant report

Variant	rs4688759
Chromosome Location	chr3:50008118-50008119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50001120..50002746-chr3:50007377..50010218,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11711814	0.85[EUR][1000 genomes]
rs11716961	0.85[EUR][1000 genomes]
rs11717829	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2023953	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]
rs2624818	0.83[EUR][1000 genomes]
rs73079018	0.82[EUR][1000 genomes]
rs73079033	0.85[EUR][1000 genomes]
rs9809001	1.00[YRI][hapmap]
rs9843677	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs9845737	0.87[AFR][1000 genomes]
rs9853352	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs9854341	1.00[ASW][hapmap]
rs9858428	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]

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	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv834689	chr3:49962930-50085119	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1012903	chr3:49978765-50071878	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs4688759	WDR6	cis	Adipose Subcutaneous	GTEx
rs4688759	PRKAR2A	cis	parietal	SCAN
rs4688759	CISH	cis	lymphoblastoid	seeQTL
rs4688759	KBTBD3	trans	parietal	SCAN
rs4688759	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs4688759	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs4688759	C3orf62	cis	cerebellum	SCAN
rs4688759	ALAS1	cis	cerebellum	SCAN
rs4688759	WDR6	cis	Whole Blood	GTEx
rs4688759	RNF123	cis	parietal	SCAN
rs4688759	WDR6	cis	Artery Tibial	GTEx
rs4688759	C3orf62	cis	parietal	SCAN
rs4688759	WDR6	cis	parietal	SCAN
rs4688759	NICN1	cis	cerebellum	SCAN
rs4688759	WDR6	cis	Esophagus Mucosa	GTEx
rs4688759	WDR6	cis	cerebellum	SCAN
rs4688759	LRRC2	cis	cerebellum	SCAN
rs4688759	RBM6	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49978800-50009600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr3:49978800-50009600	Weak transcription	Fetal Kidney	kidney
3	chr3:49978800-50041000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:49979000-50010200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:49988200-50010200	Weak transcription	Gastric	stomach
6	chr3:49988200-50010600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:49988400-50009600	Weak transcription	Fetal Brain Female	brain
8	chr3:49988400-50009600	Weak transcription	HUVEC	blood vessel
9	chr3:49992200-50037000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:49995400-50033200	Weak transcription	Fetal Brain Male	brain
11	chr3:49996600-50010200	Weak transcription	Lung	lung
12	chr3:49997000-50010600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:49997600-50009600	Weak transcription	A549	lung
14	chr3:49997800-50009600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr3:49997800-50009800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:49997800-50013800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:49998000-50078200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:49998400-50029600	Weak transcription	Fetal Heart	heart
19	chr3:49998400-50078600	Weak transcription	K562	blood
20	chr3:49998800-50019600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:49999800-50011000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr3:49999800-50028400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr3:50000000-50019600	Strong transcription	Dnd41	blood
24	chr3:50000600-50011000	Strong transcription	Primary B cells from cord blood	blood
25	chr3:50000600-50011000	Strong transcription	Primary T cells from cord blood	blood
26	chr3:50001800-50009400	Weak transcription	Brain Germinal Matrix	brain
27	chr3:50001800-50009400	Weak transcription	Placenta	Placenta
28	chr3:50002000-50009400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:50002200-50009200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:50002200-50009600	Weak transcription	Liver	Liver
31	chr3:50002200-50057000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:50002800-50009000	Weak transcription	HSMM	muscle
33	chr3:50002800-50009200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:50003000-50033400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:50003800-50014600	Weak transcription	HSMMtube	muscle
36	chr3:50004000-50008200	Strong transcription	Hela-S3	cervix
37	chr3:50004200-50008400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr3:50004200-50016000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr3:50004400-50009000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr3:50004400-50009000	Weak transcription	NH-A	brain
41	chr3:50004400-50009600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:50004400-50010200	Weak transcription	Aorta	Aorta
43	chr3:50004400-50010600	Weak transcription	NHDF-Ad	bronchial
44	chr3:50004400-50027600	Weak transcription	NHEK	skin
45	chr3:50004400-50044200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr3:50004600-50010200	Weak transcription	Colonic Mucosa	Colon
47	chr3:50004800-50009600	Weak transcription	Adipose Nuclei	Adipose
48	chr3:50004800-50009800	Weak transcription	HMEC	breast
49	chr3:50004800-50012600	Strong transcription	Fetal Intestine Small	intestine
50	chr3:50005000-50009000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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