Variant report

Variant	rs2359455
Chromosome Location	chr16:31720486-31720487
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:31719245-31721035	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:31720458-31720798	GM12878	blood:	n/a	n/a
3	POLR2A	chr16:31720303-31720883	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:31719397-31720901	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:31720301-31720882	GM12878	blood:	n/a	n/a
6	POLR2A	chr16:31718748-31725396	HepG2	liver:	n/a	n/a
7	POLR2A	chr16:31720306-31720957	HepG2	liver:	n/a	n/a
8	POLR2A	chr16:31720130-31720974	GM12891	blood:	n/a	n/a
9	POLR2A	chr16:31720299-31720769	GM12891	blood:	n/a	n/a
10	POLR2A	chr16:31719575-31720542	K562	blood:	n/a	n/a
11	POLR2A	chr16:31720435-31720887	GM12891	blood:	n/a	n/a
12	POLR2A	chr16:31718943-31727784	HepG2	liver:	n/a	n/a
13	POLR2A	chr16:31719438-31720734	GM12878	blood:	n/a	n/a
14	POLR2A	chr16:31715130-31726933	HepG2	liver:	n/a	n/a
15	POLR2A	chr16:31720332-31720896	GM12878	blood:	n/a	n/a
16	POLR2A	chr16:31718974-31728173	GM12878	blood:	n/a	n/a
17	POLR2A	chr16:31719083-31720878	GM12892	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31469625..31472736-chr16:31718738..31721377,3	K562	blood:
2	chr16:31518291..31520186-chr16:31719579..31721600,2	MCF-7	breast:
3	chr16:31467317..31473648-chr16:31720179..31727010,13	MCF-7	breast:
4	chr16:31469625..31472005-chr16:31718738..31721377,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C16orf58-5	chr16:31720434-31720634	ENSG00000261731.2

No data

Variant related genes	Relation type
ZNF720	TF binding region
ENSG00000140688	Chromatin interaction
ENSG00000260267	Chromatin interaction
ENSG00000260625	Chromatin interaction
ENSG00000140691	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10871458	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11150638	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1156903	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11644104	0.94[CEU][hapmap]
rs12324951	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12447780	0.82[ASN][1000 genomes]
rs12716999	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12717000	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1406177	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1406178	0.84[MEX][hapmap]
rs1468158	0.84[MEX][hapmap]
rs1468159	0.84[MEX][hapmap]
rs1528317	0.84[MEX][hapmap]
rs1528319	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1534507	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1852666	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1881316	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1881318	0.80[MEX][hapmap]
rs1919040	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1919042	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2078924	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2106579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2106581	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2157970	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2178179	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2188619	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2222754	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2359219	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2359222	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2359226	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28427454	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2884713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3751742	0.84[MEX][hapmap]
rs4620975	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4889553	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4889555	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4889688	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4889689	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4889693	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62054710	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6565267	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6565269	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6565275	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6565278	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6565280	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6565282	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6565285	0.93[CEU][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6565286	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6565287	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67922432	0.85[AMR][1000 genomes]
rs7188627	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7190730	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7191481	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7197963	0.84[MEX][hapmap]
rs7206536	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs727349	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8048591	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs8049323	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8053712	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8060086	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8062424	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8062902	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs916753	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs929208	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9921546	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9921898	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9928006	0.94[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9929892	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9930700	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9936002	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9938037	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
2	esv3344221	chr16:31526786-31821640	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	esv3323903	chr16:31526802-31821640	Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv3504445	chr16:31526873-31821580	Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	esv3504446	chr16:31526873-31821580	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	esv3366795	chr16:31534951-31827424	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv833195	chr16:31576112-31763222	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv1057598	chr16:31608831-31726446	Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv1067321	chr16:31652036-31959992	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv918074	chr16:31669781-31935033	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv1063037	chr16:31669981-31934894	Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv542903	chr16:31669981-31934894	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2359455	CLUHP3	cis	Whole Blood	GTEx
rs2359455	PRR14	cis	parietal	SCAN
rs2359455	TBX6	cis	parietal	SCAN
rs2359455	CD2BP2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31712600-31724200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr16:31712600-31724200	Weak transcription	Psoas Muscle	Psoas
3	chr16:31712600-31724200	Weak transcription	HSMM	muscle
4	chr16:31712800-31724200	Weak transcription	HSMMtube	muscle
5	chr16:31712800-31724200	Weak transcription	NHDF-Ad	bronchial
6	chr16:31712800-31724400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr16:31712800-31724600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr16:31713000-31724400	Weak transcription	Right Atrium	heart
9	chr16:31713200-31724000	Weak transcription	Fetal Heart	heart
10	chr16:31713200-31724200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr16:31713400-31720800	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr16:31713400-31722400	Strong transcription	Fetal Intestine Small	intestine
13	chr16:31713400-31724000	Weak transcription	K562	blood
14	chr16:31713400-31724200	Weak transcription	Fetal Brain Male	brain
15	chr16:31713600-31720800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr16:31713600-31722200	Strong transcription	Stomach Smooth Muscle	stomach
17	chr16:31713800-31720800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr16:31713800-31721400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr16:31713800-31721400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr16:31713800-31721600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr16:31713800-31721800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr16:31713800-31722200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr16:31713800-31722600	Strong transcription	Fetal Stomach	stomach
24	chr16:31714000-31720600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr16:31714000-31720600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr16:31714000-31720600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr16:31714000-31720800	Strong transcription	H9 Cell Line	embryonic stem cell
28	chr16:31714000-31720800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr16:31714000-31720800	Strong transcription	Brain Anterior Caudate	brain
30	chr16:31714000-31720800	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr16:31714000-31721400	Strong transcription	Fetal Muscle Leg	muscle
32	chr16:31714000-31721800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr16:31714000-31722800	Strong transcription	Fetal Brain Female	brain
34	chr16:31714200-31720600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr16:31714200-31721000	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr16:31714200-31721400	Strong transcription	Gastric	stomach
37	chr16:31714200-31721600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr16:31714200-31721600	Strong transcription	Fetal Intestine Large	intestine
39	chr16:31714200-31721800	Strong transcription	Liver	Liver
40	chr16:31714200-31721800	Strong transcription	GM12878-XiMat	blood
41	chr16:31714200-31722200	Strong transcription	Right Ventricle	heart
42	chr16:31714200-31722400	Strong transcription	Brain Germinal Matrix	brain
43	chr16:31714400-31720600	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr16:31714400-31720800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr16:31714400-31720800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr16:31714400-31721200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr16:31714400-31721400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr16:31714400-31721400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr16:31714400-31721400	Strong transcription	Lung	lung
50	chr16:31714600-31720600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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