Variant report

Variant	rs7209734
Chromosome Location	chr17:19988543-19988544
allele	A/C
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	HNF4A	chr17:19988359-19988624	HepG2	liver:	n/a	chr17:19988466-19988481 chr17:19988466-19988481 chr17:19988467-19988479 chr17:19988461-19988477 chr17:19988466-19988481 chr17:19988466-19988473 chr17:19988466-19988479 chr17:19988467-19988480 chr17:19988467-19988479 chr17:19988466-19988481 chr17:19988466-19988480 chr17:19988465-19988480 chr17:19988466-19988480 chr17:19988464-19988482 chr17:19988466-19988480 chr17:19988467-19988479
2	NR3C1	chr17:19988320-19988892	A549	lung:	n/a	chr17:19988519-19988535 chr17:19988735-19988756 chr17:19988577-19988592
3	CTCF	chr17:19988500-19988650	GM12871	blood:	n/a	n/a

Variant related genes	Relation type
SPECC1	TF binding region

Extended variants
information (count: 99 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10083856	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1034904	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11867585	0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11868084	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11869616	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11870111	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11871651	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs119672	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1479129	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs1638525	0.86[CHB][hapmap]
rs169412	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs175922	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs1860302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs203450	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203457	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs203458	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs203460	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203462	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs203465	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs203466	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs203477	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs203479	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs203481	0.94[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs2042046	0.85[JPT][hapmap]
rs2107565	0.80[YRI][hapmap]
rs2108978	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs2108979	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2108980	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28603224	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28637614	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28666381	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28807825	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34290687	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34291370	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34401389	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35003563	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35313716	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs36077949	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3862152	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3888318	0.95[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3909258	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs397969	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs4005937	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4267380	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4479309	0.96[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4570919	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924801	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4924803	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924806	0.96[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4925060	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs4925065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4925066	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4925067	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4925069	0.87[AMR][1000 genomes]
rs4925072	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.95[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4925073	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4925077	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925079	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925081	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925085	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56142708	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62067555	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7207625	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7208025	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7208365	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7208635	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7211535	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7218708	0.85[EUR][1000 genomes]
rs7222403	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs7223305	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8065337	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8067545	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs850623	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs860335	0.94[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs888423	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs918227	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs918228	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9889743	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9891739	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9896411	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9897246	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9897653	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9907788	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9912775	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9915758	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9944451	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv907872	chr17:19945841-19996140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1056224	chr17:19946604-19993026	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv543258	chr17:19946604-19993026	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv2762522	chr17:19976462-19996429	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7209734	SPECC1	Cis_1M	lymphoblastoid	RTeQTL
rs7209734	KRT16P3	cis	Esophagus Mucosa	GTEx
rs7209734	CYTSB	cis	cerebellum	SCAN
rs7209734	TMEM11	cis	cerebellum	SCAN
rs7209734	AKAP10	cis	lymphoblastoid	seeQTL
rs7209734	MFAP4	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19976200-19989400	Weak transcription	Lung	lung
2	chr17:19977600-19989600	Weak transcription	K562	blood
3	chr17:19978800-20000000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:19980600-19994600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr17:19980800-19990000	Weak transcription	A549	lung
6	chr17:19981200-19993000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr17:19981800-19988600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr17:19982600-19993000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr17:19983200-19993400	Weak transcription	Spleen	Spleen
10	chr17:19985000-19989400	Weak transcription	Right Ventricle	heart
11	chr17:19985600-19993000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr17:19986200-19993000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr17:19986400-19990600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr17:19986400-19991400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr17:19986800-19989200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr17:19987000-19994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr17:19987800-19988600	Enhancers	GM12878-XiMat	blood
18	chr17:19987800-19990200	Enhancers	NHDF-Ad	bronchial
19	chr17:19988000-19988600	Enhancers	Aorta	Aorta
20	chr17:19988000-19989200	Enhancers	NHLF	lung
21	chr17:19988000-19990200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr17:19988000-19990200	Enhancers	Ovary	ovary
23	chr17:19988000-19991200	Enhancers	Brain Angular Gyrus	brain
24	chr17:19988200-19988600	Genic enhancers	Primary monocytes fromperipheralblood	blood
25	chr17:19988200-19988800	Enhancers	Brain Cingulate Gyrus	brain
26	chr17:19988200-19989000	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr17:19988200-19989600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr17:19988200-19989600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr17:19988200-19990000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr17:19988200-19990200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:19988200-19990200	Enhancers	Brain Anterior Caudate	brain
32	chr17:19988200-19990200	Enhancers	Brain Hippocampus Middle	brain
33	chr17:19988200-19990200	Enhancers	Brain Substantia Nigra	brain
34	chr17:19988200-19990200	Enhancers	Left Ventricle	heart
35	chr17:19988200-19990200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr17:19988200-19990200	Enhancers	NH-A	brain
37	chr17:19988200-19990400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr17:19988200-19990400	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr17:19988200-19990400	Enhancers	Fetal Muscle Trunk	muscle
40	chr17:19988200-19990600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr17:19988200-19991000	Enhancers	HSMMtube	muscle
42	chr17:19988200-19991200	Enhancers	Adipose Nuclei	Adipose
43	chr17:19988200-19991200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr17:19988400-19988600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr17:19988400-19988600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr17:19988400-19988600	Enhancers	Pancreas	Pancrea
47	chr17:19988400-19988800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:19988400-19989200	Enhancers	Osteobl	bone
49	chr17:19988400-19989400	Enhancers	Brain Germinal Matrix	brain
50	chr17:19988400-19989600	Enhancers	HSMM	muscle

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