Variant report

Variant	rs73322309
Chromosome Location	chr17:45384410-45384411
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	FOS	chr17:45384247-45384705	MCF10A-Er-Src	breast:	n/a	n/a
2	JUND	chr17:45384296-45384670	Hela-S3	cervix:	n/a	chr17:45384420-45384431 chr17:45384475-45384486
3	JUN	chr17:45384405-45384506	HepG2	liver:	n/a	chr17:45384450-45384463
4	STAT3	chr17:45384303-45384628	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr17:45384245-45384698	MCF10A-Er-Src	breast:	n/a	n/a
6	JUND	chr17:45384338-45384596	HepG2	liver:	n/a	chr17:45384420-45384431 chr17:45384475-45384486
7	EP300	chr17:45384363-45384650	Hela-S3	cervix:	n/a	n/a
8	MYC	chr17:45384360-45384689	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr17:45384247-45384758	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr17:45384282-45384695	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr17:45384286-45384659	Hela-S3	cervix:	n/a	chr17:45384449-45384460
12	MYC	chr17:45384362-45384691	MCF10A-Er-Src	breast:	n/a	n/a
13	STAT3	chr17:45384290-45384677	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr17:45384256-45384753	MCF10A-Er-Src	breast:	n/a	n/a
15	JUN	chr17:45384310-45384713	Hela-S3	cervix:	n/a	chr17:45384450-45384463

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:

Variant related genes	Relation type
ENSG00000263293	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11079771	0.86[ASN][1000 genomes]
rs11867192	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11867253	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11867589	0.80[ASN][1000 genomes]
rs11868344	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11868912	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11869439	0.80[ASN][1000 genomes]
rs11869835	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11870176	0.80[ASN][1000 genomes]
rs11870252	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11870781	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11871031	0.80[ASN][1000 genomes]
rs11871477	0.80[ASN][1000 genomes]
rs12051664	0.80[ASN][1000 genomes]
rs12162128	0.97[ASN][1000 genomes]
rs13306485	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16941855	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16941861	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1878067	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2292700	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2317676	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3785870	0.84[ASN][1000 genomes]
rs3785873	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41304764	0.86[ASN][1000 genomes]
rs55706706	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56722403	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5919	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73322317	0.80[AFR][1000 genomes]
rs73322319	0.80[AFR][1000 genomes]
rs73322321	0.80[AFR][1000 genomes]
rs8073229	0.95[AMR][1000 genomes];0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73322309	EFCAB13	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:58 , 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	chr17:45381800-45384600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr17:45381800-45387400	Weak transcription	Placenta	Placenta
16	chr17:45381800-45387600	Weak transcription	Fetal Intestine Large	intestine
17	chr17:45381800-45392800	Weak transcription	Left Ventricle	heart
18	chr17:45382200-45385000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr17:45382200-45385200	Enhancers	Hela-S3	cervix
20	chr17:45382400-45385000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr17:45382400-45385000	Enhancers	HMEC	breast
22	chr17:45382600-45385000	Enhancers	NHEK	skin
23	chr17:45382800-45384800	Weak transcription	Fetal Stomach	stomach
24	chr17:45382800-45387400	Weak transcription	Aorta	Aorta
25	chr17:45382800-45394600	Weak transcription	Small Intestine	intestine
26	chr17:45382800-45400800	Weak transcription	Lung	lung
27	chr17:45383000-45388400	Weak transcription	Spleen	Spleen
28	chr17:45383000-45389600	Strong transcription	Fetal Muscle Leg	muscle
29	chr17:45383200-45384600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr17:45383200-45384600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr17:45383200-45387400	Weak transcription	K562	blood
32	chr17:45383200-45387600	Weak transcription	Fetal Heart	heart
33	chr17:45383600-45384600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr17:45383600-45384800	Weak transcription	Colon Smooth Muscle	Colon
35	chr17:45383600-45387600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr17:45383600-45387800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr17:45383600-45392400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr17:45383600-45392600	Weak transcription	Adipose Nuclei	Adipose
39	chr17:45383800-45384600	Weak transcription	Osteobl	bone
40	chr17:45383800-45384800	Weak transcription	HSMMtube	muscle
41	chr17:45383800-45385000	Weak transcription	NHDF-Ad	bronchial
42	chr17:45383800-45385200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr17:45383800-45386400	Weak transcription	Ovary	ovary
44	chr17:45383800-45387400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr17:45383800-45387800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr17:45383800-45387800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr17:45383800-45391000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:45383800-45391200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr17:45383800-45392000	Weak transcription	HSMM	muscle
50	chr17:45383800-45392000	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links