Variant report

Variant	rs16941861
Chromosome Location	chr17:45383619-45383620
allele	A/G
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	NFIC	chr17:45382397-45383623	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45377393..45379681-chr17:45383404..45387690,4	K562	blood:
2	chr17:45382065..45383991-chr17:45399117..45400961,2	K562	blood:

Variant related genes	Relation type
ENSG00000263293	TF binding region
ENSG00000178852	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11079771	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11867192	1.00[CEU][hapmap];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]
rs11867253	1.00[CEU][hapmap];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]
rs11867589	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs11868344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868912	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11869439	1.00[JPT][hapmap]
rs11869768	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs11869835	1.00[CEU][hapmap];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]
rs11870252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11870781	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[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]
rs11871031	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs11871477	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs12051664	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs12051702	1.00[JPT][hapmap]
rs12162128	0.98[ASN][1000 genomes]
rs13306485	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16941751	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs16941771	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs16941855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878067	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2292700	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2317676	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]
rs3785870	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3785873	1.00[CEU][hapmap];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]
rs41304764	0.88[ASN][1000 genomes]
rs55706706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56722403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5919	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73322309	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8073229	0.82[CEU][hapmap];0.81[CHB][hapmap];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16941861	EFCAB13	cis	Skin Sun Exposed Lower leg	GTEx
rs16941861	C17orf57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 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	chr17:45381200-45383800	Enhancers	NHDF-Ad	bronchial
14	chr17:45381400-45383800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:45381400-45392600	Weak transcription	Liver	Liver
16	chr17:45381600-45383800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr17:45381600-45384000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr17:45381600-45384400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr17:45381800-45384600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr17:45381800-45387400	Weak transcription	Placenta	Placenta
21	chr17:45381800-45387600	Weak transcription	Fetal Intestine Large	intestine
22	chr17:45381800-45392800	Weak transcription	Left Ventricle	heart
23	chr17:45382200-45383800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr17:45382200-45384000	Enhancers	NHLF	lung
25	chr17:45382200-45385000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr17:45382200-45385200	Enhancers	Hela-S3	cervix
27	chr17:45382400-45383800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr17:45382400-45383800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr17:45382400-45383800	Enhancers	Stomach Mucosa	stomach
30	chr17:45382400-45383800	Enhancers	HSMM	muscle
31	chr17:45382400-45383800	Enhancers	HSMMtube	muscle
32	chr17:45382400-45383800	Enhancers	Osteobl	bone
33	chr17:45382400-45384000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr17:45382400-45384000	Enhancers	Muscle Satellite Cultured Cells	--
35	chr17:45382400-45384000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr17:45382400-45385000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr17:45382400-45385000	Enhancers	HMEC	breast
38	chr17:45382600-45383800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr17:45382600-45383800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr17:45382600-45383800	Enhancers	Primary T cells fromperipheralblood	blood
41	chr17:45382600-45383800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr17:45382600-45383800	Enhancers	Ovary	ovary
43	chr17:45382600-45383800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr17:45382600-45385000	Enhancers	NHEK	skin
45	chr17:45382800-45383800	Weak transcription	Right Atrium	heart
46	chr17:45382800-45383800	Enhancers	HepG2	liver
47	chr17:45382800-45384800	Weak transcription	Fetal Stomach	stomach
48	chr17:45382800-45387400	Weak transcription	Aorta	Aorta
49	chr17:45382800-45394600	Weak transcription	Small Intestine	intestine
50	chr17:45382800-45400800	Weak transcription	Lung	lung

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