Variant report

Variant	rs5919
Chromosome Location	chr17:45364540-45364541
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	TBP	chr17:45363518-45364882	GM12878	blood:	n/a	n/a
2	YY1	chr17:45364436-45364811	GM12892	blood:	n/a	n/a
3	CEBPB	chr17:45363307-45364941	GM12878	blood:	n/a	n/a
4	CTCF	chr17:45364500-45364650	GM12868	blood:	n/a	n/a
5	CTCF	chr17:45364520-45364670	GM12866	blood:	n/a	n/a
6	POLR2A	chr17:45363387-45364754	GM12892	blood:	n/a	n/a
7	CTCF	chr17:45364485-45364739	GM12878	blood:	n/a	n/a
8	CTCF	chr17:45364440-45364590	GM12869	blood:	n/a	n/a
9	TBL1XR1	chr17:45363539-45364561	GM12878	blood:	n/a	n/a
10	FOXM1	chr17:45363369-45364809	GM12878	blood:	n/a	n/a
11	FOXM1	chr17:45363298-45364683	GM12878	blood:	n/a	n/a
12	CTCF	chr17:45364500-45364650	GM12873	blood:	n/a	n/a
13	RELA	chr17:45363413-45364650	GM18505	blood:	n/a	n/a
14	ZNF143	chr17:45364458-45364789	GM12878	blood:	n/a	n/a
15	RAD21	chr17:45363474-45364808	GM12878	blood:	n/a	chr17:45364010-45364020
16	RCOR1	chr17:45363377-45364787	GM12878	blood:	n/a	n/a
17	CTCF	chr17:45364486-45364713	GM19238	blood:	n/a	n/a
18	CTCF	chr17:45364540-45364690	GM12864	blood:	n/a	n/a
19	CTCF	chr17:45364498-45364725	GM12891	blood:	n/a	n/a
20	EP300	chr17:45363445-45364576	GM12878	blood:	n/a	n/a
21	YY1	chr17:45363551-45364849	GM12878	blood:	n/a	n/a
22	CTCF	chr17:45364500-45364650	GM12870	blood:	n/a	n/a
23	EP300	chr17:45363474-45364782	GM12878	blood:	n/a	n/a
24	CTCF	chr17:45364485-45364734	GM12892	blood:	n/a	n/a
25	MTA3	chr17:45363092-45365063	GM12878	blood:	n/a	n/a
26	WRNIP1	chr17:45363344-45364718	GM12878	blood:	n/a	n/a
27	RAD21	chr17:45364471-45364781	GM12878	blood:	n/a	n/a
28	BCLAF1	chr17:45363457-45364867	GM12878	blood:	n/a	n/a
29	NFATC1	chr17:45363337-45364715	GM12878	blood:	n/a	n/a
30	RELA	chr17:45363582-45365199	GM18951	blood:	n/a	n/a
31	SMC3	chr17:45363346-45364879	GM12878	blood:	n/a	n/a
32	CTCF	chr17:45364540-45364690	GM12872	blood:	n/a	n/a
33	CTCF	chr17:45364480-45364630	GM12878	blood:	n/a	n/a
34	POLR2A	chr17:45363538-45365548	GM12878	blood:	n/a	n/a
35	MAX	chr17:45363322-45364729	GM12878	blood:	n/a	n/a
36	CTCF	chr17:45364460-45364610	GM12801	blood:	n/a	n/a
37	STAT5A	chr17:45363379-45364654	GM12878	blood:	n/a	chr17:45363611-45363623 chr17:45363839-45363851
38	ATF2	chr17:45363251-45364686	GM12878	blood:	n/a	n/a
39	RAD21	chr17:45364465-45364693	GM12878	blood:	n/a	n/a
40	STAT5A	chr17:45363487-45364769	GM12878	blood:	n/a	chr17:45363611-45363623 chr17:45363839-45363851
41	CTCF	chr17:45364521-45364699	GM19240	blood:	n/a	n/a
42	CHD2	chr17:45363483-45364769	GM12878	blood:	n/a	n/a
43	CTCF	chr17:45364540-45364690	GM12874	blood:	n/a	n/a
44	CTCF	chr17:45364540-45364690	GM12870	blood:	n/a	n/a
45	CTCF	chr17:45364480-45364630	HCM	heart:	n/a	n/a
46	EBF1	chr17:45363348-45364863	GM12878	blood:	n/a	chr17:45364008-45364017 chr17:45364008-45364018 chr17:45364006-45364019 chr17:45364007-45364018
47	CTCF	chr17:45364539-45364698	GM13977	blood:	n/a	n/a
48	NFATC1	chr17:45363528-45364662	GM12878	blood:	n/a	n/a
49	RELA	chr17:45363575-45364688	GM19099	blood:	n/a	n/a
50	EBF1	chr17:45363443-45364825	GM12878	blood:	n/a	chr17:45364008-45364017 chr17:45364008-45364018 chr17:45364006-45364019 chr17:45364007-45364018

No.	Distal block	Cell Line	Cell type
1	chr17:45363175..45368028-chr17:45369299..45373237,4	K562	blood:
2	chr17:45332159..45334737-chr17:45364459..45366214,2	K562	blood:
3	chr17:45360332..45367497-chr17:45367923..45374401,11	K562	blood:

Variant related genes	Relation type
ITGB3	TF binding region
ENSG00000259207	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11079771	0.87[CHB][hapmap]
rs11867192	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11867253	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11868344	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11868912	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11869835	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11870252	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11870781	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12051795	1.00[JPT][hapmap]
rs13306485	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941751	0.81[CHB][hapmap]
rs16941771	0.81[CHB][hapmap]
rs16941855	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16941861	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1878067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317676	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]
rs3785870	0.87[CHB][hapmap]
rs3785873	0.82[CEU][hapmap];0.81[CHB][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55706706	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56722403	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73322309	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8064871	0.93[ASN][1000 genomes]
rs8073179	0.86[ASN][1000 genomes]
rs8073229	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077238	0.90[ASN][1000 genomes]
rs8077375	0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][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
rs5919	C17orf57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45354600-45372000	Weak transcription	Esophagus	oesophagus
2	chr17:45356800-45377200	Weak transcription	Fetal Intestine Large	intestine
3	chr17:45357200-45371600	Weak transcription	Right Ventricle	heart
4	chr17:45357200-45398000	Weak transcription	Psoas Muscle	Psoas
5	chr17:45357800-45365800	Weak transcription	Ovary	ovary
6	chr17:45357800-45365800	Weak transcription	HSMMtube	muscle
7	chr17:45357800-45369400	Weak transcription	Fetal Intestine Small	intestine
8	chr17:45358200-45365000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:45358200-45366000	Weak transcription	Right Atrium	heart
10	chr17:45358200-45367600	Weak transcription	Adipose Nuclei	Adipose
11	chr17:45358200-45371800	Weak transcription	Colonic Mucosa	Colon
12	chr17:45358200-45377200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr17:45358400-45365800	Weak transcription	NH-A	brain
14	chr17:45358400-45366000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr17:45358600-45371000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr17:45358800-45366000	Weak transcription	Lung	lung
17	chr17:45359000-45371600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr17:45359000-45372000	Weak transcription	Left Ventricle	heart
19	chr17:45359000-45389800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr17:45359800-45371200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr17:45360000-45364600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr17:45360000-45366000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr17:45360400-45371800	Strong transcription	Colon Smooth Muscle	Colon
24	chr17:45360600-45373800	Strong transcription	Fetal Stomach	stomach
25	chr17:45360800-45371800	Strong transcription	Fetal Muscle Leg	muscle
26	chr17:45361400-45370000	Strong transcription	Aorta	Aorta
27	chr17:45361400-45371400	Strong transcription	Stomach Smooth Muscle	stomach
28	chr17:45361800-45367400	Strong transcription	Placenta	Placenta
29	chr17:45361800-45368200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr17:45362800-45370800	Weak transcription	HUVEC	blood vessel
31	chr17:45363000-45365800	Enhancers	K562	blood
32	chr17:45363000-45366600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr17:45363200-45364800	Strong transcription	Rectal Smooth Muscle	rectum
34	chr17:45363200-45366000	Enhancers	Primary B cells from peripheral blood	blood
35	chr17:45363200-45368000	Weak transcription	Liver	Liver
36	chr17:45363400-45364600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr17:45363400-45365200	Flanking Active TSS	GM12878-XiMat	blood
38	chr17:45363600-45364800	Enhancers	Spleen	Spleen
39	chr17:45363600-45364800	Enhancers	HSMM	muscle
40	chr17:45363600-45365000	Genic enhancers	NHDF-Ad	bronchial
41	chr17:45363600-45366200	Enhancers	Primary B cells from cord blood	blood
42	chr17:45363800-45364600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr17:45363800-45365800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr17:45363800-45366000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr17:45363800-45366400	Strong transcription	Fetal Heart	heart
46	chr17:45364000-45364600	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr17:45364000-45364600	Enhancers	Brain Hippocampus Middle	brain
48	chr17:45364000-45364600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
49	chr17:45364000-45365000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr17:45364000-45365800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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