Variant report

Variant	rs1052352
Chromosome Location	chr16:31195279-31195280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:31194158-31195799	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:31194388-31195893	K562	blood:	n/a	n/a
3	POLR2A	chr16:31194920-31196071	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:31194732-31195710	GM12891	blood:	n/a	n/a
5	TBL1XR1	chr16:31194723-31195411	GM12878	blood:	n/a	n/a
6	POLR2A	chr16:31195046-31195795	K562	blood:	n/a	n/a
7	WRNIP1	chr16:31194814-31195537	GM12878	blood:	n/a	n/a
8	POLR2A	chr16:31195178-31195435	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr16:31190660-31197223	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr16:31194726-31195292	U87	brain:	n/a	n/a
11	POLR2A	chr16:31194750-31195735	HepG2	liver:	n/a	n/a
12	POLR2A	chr16:31194957-31195753	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr16:31194383-31195702	HepG2	liver:	n/a	n/a
14	POU2F2	chr16:31195080-31195769	GM12878	blood:	n/a	n/a
15	POLR2A	chr16:31194246-31195737	GM12891	blood:	n/a	n/a
16	POLR2A	chr16:31194702-31195784	GM12891	blood:	n/a	n/a
17	POLR2A	chr16:31194874-31195646	PFSK-1	brain:	n/a	n/a
18	POLR2A	chr16:31190908-31195723	K562	blood:	n/a	n/a
19	POLR2A	chr16:31194729-31195721	K562	blood:	n/a	n/a
20	POLR2A	chr16:31190153-31195916	GM12878	blood:	n/a	n/a
21	POLR2A	chr16:31195265-31195691	HepG2	liver:	n/a	n/a
22	POLR2A	chr16:31193491-31195932	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr16:31195111-31195806	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr16:31194712-31195754	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr16:31190296-31214398	PANC-1	pancreas:	n/a	n/a
26	HEY1	chr16:31194720-31195595	HepG2	liver:	n/a	n/a
27	POLR2A	chr16:31195138-31195504	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr16:31195130-31195761	HL-60	blood:	n/a	n/a
29	POLR2A	chr16:31190139-31214678	GM12878	blood:	n/a	n/a
30	HEY1	chr16:31195201-31195689	K562	blood:	n/a	n/a
31	POLR2A	chr16:31195229-31195587	MCF-7	breast:	n/a	n/a
32	POLR2A	chr16:31194726-31195793	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr16:31193765-31195835	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr16:31195110-31195717	GM12878	blood:	n/a	n/a
35	POLR2A	chr16:31193371-31195872	GM12892	blood:	n/a	n/a
36	POLR2A	chr16:31190778-31195905	GM12892	blood:	n/a	n/a
37	POLR2A	chr16:31190225-31195735	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr16:31194673-31195864	GM12891	blood:	n/a	n/a
39	POLR2A	chr16:31193512-31195756	A549	lung:	n/a	n/a
40	POLR2A	chr16:31190516-31195882	GM12892	blood:	n/a	n/a
41	POLR2A	chr16:31195215-31195727	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr16:31194810-31195614	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr16:31193590-31195760	GM12878	blood:	n/a	n/a
44	POLR2A	chr16:31194750-31195858	K562	blood:	n/a	n/a
45	POLR2A	chr16:31195173-31195738	GM12878	blood:	n/a	n/a
46	POLR2A	chr16:31194810-31195748	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr16:31194648-31195717	GM12892	blood:	n/a	n/a
48	POLR2A	chr16:31194712-31195752	GM12878	blood:	n/a	n/a
49	HEY1	chr16:31191184-31195940	K562	blood:	n/a	chr16:31191879-31191894 chr16:31191563-31191578 chr16:31191399-31191414 chr16:31191657-31191672 chr16:31191575-31191590
50	POLR2A	chr16:31193758-31195831	GM12891	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31149707..31163529-chr16:31187237..31198825,44	K562	blood:
2	chr16:31151687..31162079-chr16:31189046..31201898,43	K562	blood:
3	chr16:31043806..31046145-chr16:31195048..31197092,2	K562	blood:
4	chr16:31149322..31163059-chr16:31188531..31198512,46	MCF-7	breast:
5	chr16:31195044..31196734-chr16:31471176..31472884,2	K562	blood:
6	chr16:31126872..31130668-chr16:31190197..31195425,8	MCF-7	breast:
7	chr16:31083048..31086004-chr16:31194000..31195518,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260304	TF binding region
FUS	TF binding region
ENSG00000103510	Chromatin interaction
ENSG00000167395	Chromatin interaction
ENSG00000178226	Chromatin interaction
ENSG00000167394	Chromatin interaction
ENSG00000140691	Chromatin interaction
ENSG00000262766	Chromatin interaction
ENSG00000103496	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11641624	0.82[JPT][hapmap]
rs11645526	0.83[JPT][hapmap]
rs11864632	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12929077	0.82[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs13333997	0.89[ASN][1000 genomes]
rs17708638	0.86[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap]
rs2288005	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2735393	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3764323	0.96[ASN][1000 genomes]
rs3764327	0.83[JPT][hapmap]
rs4496161	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4889537	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4889538	0.98[ASN][1000 genomes]
rs4889623	0.84[CEU][hapmap]
rs4889633	0.96[ASN][1000 genomes]
rs4889640	0.82[GIH][hapmap];0.83[JPT][hapmap]
rs57348955	0.91[ASN][1000 genomes]
rs7184910	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7186832	0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7187143	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7193943	0.83[JPT][hapmap]
rs741810	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8056505	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8057320	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
4	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
5	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
6	nsv905740	chr16:31066249-31232437	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
7	nsv905741	chr16:31066249-31247924	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
8	nsv905742	chr16:31102321-31247924	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	188 gene(s)	inside rSNPs	diseases
9	nsv542900	chr16:31137352-31197027	Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1052352	YPEL3	cis	cerebellum	SCAN
rs1052352	ITGAX	cis	cerebellum	SCAN
rs1052352	MYST1	cis	parietal	SCAN
rs1052352	ZNF668	cis	cerebellum	SCAN
rs1052352	TBX6	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31192400-31195400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:31192400-31195400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
3	chr16:31192400-31195800	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr16:31192600-31195400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr16:31192600-31195400	Transcr. at gene 5' and 3'	A549	lung
6	chr16:31192600-31195600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
7	chr16:31192600-31195800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
8	chr16:31192800-31195600	Transcr. at gene 5' and 3'	Hela-S3	cervix
9	chr16:31192800-31195600	Transcr. at gene 5' and 3'	Osteobl	bone
10	chr16:31193000-31195600	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
11	chr16:31193000-31196800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr16:31193200-31195600	Genic enhancers	Brain Substantia Nigra	brain
13	chr16:31193200-31200000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr16:31193400-31195400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
15	chr16:31193400-31195600	Genic enhancers	Primary B cells from peripheral blood	blood
16	chr16:31193400-31198600	Genic enhancers	Primary monocytes fromperipheralblood	blood
17	chr16:31193600-31195400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr16:31193600-31195600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
19	chr16:31193600-31195800	Genic enhancers	Placenta	Placenta
20	chr16:31193800-31195400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr16:31193800-31195400	Genic enhancers	Brain Cingulate Gyrus	brain
22	chr16:31193800-31195400	Genic enhancers	Spleen	Spleen
23	chr16:31193800-31195400	Transcr. at gene 5' and 3'	NHLF	lung
24	chr16:31193800-31195600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr16:31193800-31195600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr16:31193800-31195600	Genic enhancers	Lung	lung
27	chr16:31193800-31195800	Genic enhancers	Pancreas	Pancrea
28	chr16:31193800-31197000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr16:31193800-31197800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr16:31194000-31195400	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
31	chr16:31194000-31195400	Genic enhancers	Colon Smooth Muscle	Colon
32	chr16:31194000-31195400	Genic enhancers	Duodenum Mucosa	Duodenum
33	chr16:31194000-31195400	Genic enhancers	Fetal Brain Male	brain
34	chr16:31194000-31195400	Genic enhancers	Fetal Muscle Leg	muscle
35	chr16:31194000-31195400	Genic enhancers	Fetal Stomach	stomach
36	chr16:31194000-31195400	Genic enhancers	Gastric	stomach
37	chr16:31194000-31195600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr16:31194000-31195600	Genic enhancers	Brain Anterior Caudate	brain
39	chr16:31194000-31195600	Genic enhancers	Brain Hippocampus Middle	brain
40	chr16:31194000-31195600	Genic enhancers	Fetal Muscle Trunk	muscle
41	chr16:31194000-31195800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr16:31194000-31195800	Genic enhancers	Liver	Liver
43	chr16:31194000-31197000	Genic enhancers	Monocytes-CD14+_RO01746	blood
44	chr16:31194200-31195400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
45	chr16:31194200-31195600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr16:31194200-31195600	Genic enhancers	Primary B cells from cord blood	blood
47	chr16:31194200-31195600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr16:31194200-31195600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
49	chr16:31194200-31195600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr16:31194200-31195600	Genic enhancers	Left Ventricle	heart

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