Variant report

Variant	rs3809863
Chromosome Location	chr17:45385012-45385013
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45384246..45386352-chr17:45388308..45390190,2	K562	blood:
2	chr17:45373564..45376277-chr17:45383806..45386110,2	K562	blood:
3	chr17:45377393..45379681-chr17:45383404..45387690,4	K562	blood:
4	chr17:45384852..45386480-chr17:45387165..45389808,2	K562	blood:
5	chr17:45377393..45380597-chr17:45384667..45388953,5	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11079774	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11650072	0.86[YRI][hapmap]
rs11655943	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12452315	0.94[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.89[YRI][hapmap]
rs12452796	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap]
rs12600603	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12603582	0.94[CHB][hapmap];0.82[CHD][hapmap];0.86[ASN][1000 genomes]
rs1912482	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs1912483	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2175290	0.87[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap]
rs2317631	0.81[ASN][1000 genomes]
rs35016056	0.81[ASN][1000 genomes]
rs4968317	0.85[ASN][1000 genomes]
rs4968319	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap]
rs62076461	0.81[ASN][1000 genomes]
rs6504833	0.86[YRI][hapmap]
rs6504872	0.94[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs7206971	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[ASN][1000 genomes]
rs7209109	0.86[ASN][1000 genomes]
rs7214410	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs7214468	0.86[YRI][hapmap]
rs7220606	0.83[AMR][1000 genomes]
rs7221196	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9303533	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9674670	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9889709	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs9893901	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs9912311	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs9912450	0.82[AFR][1000 genomes]
rs9915919	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]

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	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs3809863	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs3809863	MRPL45P2	cis	lymphoblastoid	seeQTL
rs3809863	SP6	cis	multi-tissue	Pritchard
rs3809863	NPEPPS	cis	parietal	SCAN
rs3809863	KRT33A	cis	parietal	SCAN
rs3809863	RAB5C	cis	parietal	SCAN
rs3809863	DBF4B	cis	cerebellum	SCAN
rs3809863	AL832820	cis	multi-tissue	Pritchard
rs3809863	CC2D2A	cis	Liver	GTEx
rs3809863	AL512720	trans	multi-tissue	Pritchard
rs3809863	hCT1830328.2	trans	multi-tissue	Pritchard
rs3809863	TBKBP1	cis	Nerve Tibial	GTEx
rs3809863	NBR2	cis	cerebellum	SCAN
rs3809863	VPS25	cis	cerebellum	SCAN
rs3809863	C17orf57	cis	cerebellum	SCAN
rs3809863	Contig59481_RC	cis	multi-tissue	Pritchard
rs3809863	C17orf65	cis	cerebellum	SCAN
rs3809863	C17orf57	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45357200-45398000	Weak transcription	Psoas Muscle	Psoas
2	chr17:45359000-45389800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr17:45371400-45393000	Weak transcription	Dnd41	blood
4	chr17:45372400-45389600	Weak transcription	Esophagus	oesophagus
5	chr17:45372400-45389800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr17:45372400-45394400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:45374000-45392800	Weak transcription	Brain Substantia Nigra	brain
8	chr17:45375400-45388400	Strong transcription	Fetal Muscle Trunk	muscle
9	chr17:45376200-45389200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr17:45379600-45390400	Weak transcription	Fetal Intestine Small	intestine
11	chr17:45380200-45392800	Weak transcription	Brain Hippocampus Middle	brain
12	chr17:45380400-45387800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr17:45381400-45392600	Weak transcription	Liver	Liver
14	chr17:45381800-45387400	Weak transcription	Placenta	Placenta
15	chr17:45381800-45387600	Weak transcription	Fetal Intestine Large	intestine
16	chr17:45381800-45392800	Weak transcription	Left Ventricle	heart
17	chr17:45382200-45385200	Enhancers	Hela-S3	cervix
18	chr17:45382800-45387400	Weak transcription	Aorta	Aorta
19	chr17:45382800-45394600	Weak transcription	Small Intestine	intestine
20	chr17:45382800-45400800	Weak transcription	Lung	lung
21	chr17:45383000-45388400	Weak transcription	Spleen	Spleen
22	chr17:45383000-45389600	Strong transcription	Fetal Muscle Leg	muscle
23	chr17:45383200-45387400	Weak transcription	K562	blood
24	chr17:45383200-45387600	Weak transcription	Fetal Heart	heart
25	chr17:45383600-45387600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr17:45383600-45387800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr17:45383600-45392400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr17:45383600-45392600	Weak transcription	Adipose Nuclei	Adipose
29	chr17:45383800-45385200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr17:45383800-45386400	Weak transcription	Ovary	ovary
31	chr17:45383800-45387400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr17:45383800-45387800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr17:45383800-45387800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr17:45383800-45391000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr17:45383800-45391200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr17:45383800-45392000	Weak transcription	HSMM	muscle
37	chr17:45383800-45392000	Weak transcription	NH-A	brain
38	chr17:45383800-45392200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr17:45384000-45390000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr17:45384000-45392000	Weak transcription	NHLF	lung
41	chr17:45384400-45385200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr17:45384400-45385200	Enhancers	Stomach Mucosa	stomach
43	chr17:45384400-45385400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr17:45384600-45385200	Enhancers	Placenta Amnion	Placenta Amnion
45	chr17:45384600-45385800	Strong transcription	Osteobl	bone
46	chr17:45384600-45386200	Strong transcription	Stomach Smooth Muscle	stomach
47	chr17:45384600-45389000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr17:45384800-45385200	Strong transcription	HSMMtube	muscle
49	chr17:45384800-45385200	Strong transcription	HUVEC	blood vessel
50	chr17:45384800-45389000	Strong transcription	Colon Smooth Muscle	Colon

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