Variant report

Variant	rs2317676
Chromosome Location	chr17:45388283-45388284
allele	A/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: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	chr17:45386706..45389041-chr17:45392515..45394935,2	K562	blood:
2	chr17:45384852..45386480-chr17:45387165..45389808,2	K562	blood:
3	chr17:45264770..45266603-chr17:45386177..45388793,2	K562	blood:
4	chr17:45386819..45389331-chr17:45399476..45402674,3	K562	blood:
5	chr17:45315467..45317488-chr17:45387881..45390169,2	MCF-7	breast:
6	chr17:45386092..45388850-chr17:45390487..45392389,2	K562	blood:
7	chr17:45377393..45380597-chr17:45384667..45388953,5	K562	blood:
8	chr17:45386047..45389088-chr17:45398198..45402179,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000263293	Chromatin interaction
ENSG00000178852	Chromatin interaction
ENSG00000004897	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11079771	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11867192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11867253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11867589	0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11868344	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11868912	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11869439	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11869768	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs11869835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11870176	0.81[ASN][1000 genomes]
rs11870252	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11870781	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11871031	0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11871477	0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12051664	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12051702	1.00[JPT][hapmap]
rs12162128	0.96[ASN][1000 genomes]
rs13306485	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16941751	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs16941771	0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs16941855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16941861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1878067	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2292700	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3785870	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3785873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41304764	0.85[ASN][1000 genomes]
rs55706706	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56722403	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5919	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73322309	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8073229	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2317676	C17orf57	Cis_1M	lymphoblastoid	RTeQTL
rs2317676	EFCAB13	cis	Adipose Subcutaneous	GTEx
rs2317676	EFCAB13	cis	Esophagus Mucosa	GTEx

Chromatin state (count:59 , 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	chr17:45381400-45392600	Weak transcription	Liver	Liver
13	chr17:45381800-45392800	Weak transcription	Left Ventricle	heart
14	chr17:45382800-45394600	Weak transcription	Small Intestine	intestine
15	chr17:45382800-45400800	Weak transcription	Lung	lung
16	chr17:45383000-45388400	Weak transcription	Spleen	Spleen
17	chr17:45383000-45389600	Strong transcription	Fetal Muscle Leg	muscle
18	chr17:45383600-45392400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr17:45383600-45392600	Weak transcription	Adipose Nuclei	Adipose
20	chr17:45383800-45391000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:45383800-45391200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr17:45383800-45392000	Weak transcription	HSMM	muscle
23	chr17:45383800-45392000	Weak transcription	NH-A	brain
24	chr17:45383800-45392200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:45384000-45390000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr17:45384000-45392000	Weak transcription	NHLF	lung
27	chr17:45384600-45389000	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr17:45384800-45389000	Strong transcription	Colon Smooth Muscle	Colon
29	chr17:45384800-45389200	Strong transcription	Fetal Stomach	stomach
30	chr17:45385000-45388400	Strong transcription	NHDF-Ad	bronchial
31	chr17:45385000-45391200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr17:45385000-45392600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr17:45385200-45392000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr17:45385400-45391600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr17:45387200-45390000	Strong transcription	HUVEC	blood vessel
36	chr17:45387400-45388600	Strong transcription	Aorta	Aorta
37	chr17:45387400-45388800	Strong transcription	HSMMtube	muscle
38	chr17:45387400-45388800	Strong transcription	Osteobl	bone
39	chr17:45387400-45389400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr17:45387400-45389800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr17:45387600-45388400	Enhancers	H1 Cell Line	embryonic stem cell
42	chr17:45387600-45388400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr17:45387600-45388400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr17:45387600-45388600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr17:45387600-45388600	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr17:45387600-45388600	Genic enhancers	Placenta	Placenta
47	chr17:45387600-45388800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr17:45387600-45389000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr17:45387600-45390200	Strong transcription	Fetal Heart	heart
50	chr17:45387800-45388600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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