Variant report

Variant	rs2735393
Chromosome Location	chr16:31196105-31196106
allele	C/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:7)
LncRNA
region (count:0)
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	chr16:31195959-31204084	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr16:31196095-31197234	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr16:31196099-31214010	K562	blood:	n/a	n/a
4	POLR2A	chr16:31196046-31214408	GM12892	blood:	n/a	n/a
5	POLR2A	chr16:31190660-31197223	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr16:31195965-31196277	GM12891	blood:	n/a	n/a
7	POLR2A	chr16:31195988-31211763	HepG2	liver:	n/a	n/a
8	POLR2A	chr16:31190296-31214398	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr16:31190139-31214678	GM12878	blood:	n/a	n/a
10	POLR2A	chr16:31195976-31196183	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr16:31196065-31203826	GM12878	blood:	n/a	n/a
12	HEY1	chr16:31195960-31200674	K562	blood:	n/a	chr16:31196925-31196934
13	POLR2A	chr16:31195941-31197193	GM12891	blood:	n/a	n/a
14	POLR2A	chr16:31195969-31215569	GM12878	blood:	n/a	n/a
15	POLR2A	chr16:31196034-31207331	K562	blood:	n/a	n/a
16	POLR2A	chr16:31195920-31214747	GM12892	blood:	n/a	n/a
17	POLR2A	chr16:31195966-31208486	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr16:31141772..31145245-chr16:31195885..31201101,4	MCF-7	breast:
2	chr16:31149707..31163529-chr16:31187237..31198825,44	K562	blood:
3	chr16:31151687..31162079-chr16:31189046..31201898,43	K562	blood:
4	chr16:31127731..31130553-chr16:31195379..31197872,3	K562	blood:
5	chr16:31043806..31046145-chr16:31195048..31197092,2	K562	blood:
6	chr16:31149322..31163059-chr16:31188531..31198512,46	MCF-7	breast:
7	chr16:31195044..31196734-chr16:31471176..31472884,2	K562	blood:

No data

Variant related genes	Relation type
FUS	TF binding region
ENSG00000260304	TF binding region
ENSG00000103496	Chromatin interaction
ENSG00000103510	Chromatin interaction
ENSG00000261385	Chromatin interaction
ENSG00000262766	Chromatin interaction
ENSG00000178226	Chromatin interaction
ENSG00000140691	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1052352	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11641624	0.82[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs11645526	0.87[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap]
rs11864632	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12926743	0.89[EUR][1000 genomes]
rs12929077	1.00[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12935054	0.91[EUR][1000 genomes]
rs13333997	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13336592	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs17708638	0.82[ASW][hapmap];0.87[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2288005	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3764323	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3764327	0.87[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap]
rs3815801	0.83[CEU][hapmap]
rs4496161	0.92[ASN][1000 genomes]
rs4561481	0.81[EUR][1000 genomes]
rs4889537	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889538	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889633	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4889640	0.96[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs57348955	0.90[ASN][1000 genomes]
rs7184910	0.93[ASN][1000 genomes]
rs7186832	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7187143	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7193943	0.87[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap]
rs741810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7499192	0.82[GIH][hapmap]
rs8048583	0.87[CEU][hapmap];0.82[GIH][hapmap]
rs8051304	0.81[EUR][1000 genomes]
rs8056505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8057320	0.87[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap]
rs8062426	0.81[EUR][1000 genomes]
rs889551	0.83[AMR][1000 genomes]
rs9923270	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]

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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2735393	YPEL3	cis	parietal	SCAN
rs2735393	FUS	cis	cerebellum	SCAN
rs2735393	PYDC1	cis	Skin Sun Exposed Lower leg	GTEx
rs2735393	RABEP2	cis	cerebellum	SCAN
rs2735393	QPRT	cis	cerebellum	SCAN
rs2735393	ITGAX	cis	lymphoblastoid	seeQTL
rs2735393	CD19	cis	cerebellum	SCAN
rs2735393	ITGAM	cis	lymphoblastoid	seeQTL
rs2735393	MYST1	cis	parietal	SCAN
rs2735393	TUFM	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31193000-31196800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:31193200-31200000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr16:31193400-31198600	Genic enhancers	Primary monocytes fromperipheralblood	blood
4	chr16:31193800-31197000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr16:31193800-31197800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr16:31194000-31197000	Genic enhancers	Monocytes-CD14+_RO01746	blood
7	chr16:31194200-31196400	Genic enhancers	Ovary	ovary
8	chr16:31194200-31197600	Weak transcription	Stomach Mucosa	stomach
9	chr16:31194200-31197800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr16:31194200-31197800	Genic enhancers	Fetal Thymus	thymus
11	chr16:31194200-31198200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr16:31194200-31200000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr16:31194200-31205800	Strong transcription	Small Intestine	intestine
14	chr16:31194200-31208000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr16:31194200-31208200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr16:31194400-31197600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr16:31194400-31199800	Genic enhancers	Thymus	Thymus
18	chr16:31194400-31200200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr16:31194400-31201200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr16:31194400-31201800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr16:31194400-31202600	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr16:31194400-31208200	Strong transcription	HSMMtube	muscle
23	chr16:31194400-31208400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
24	chr16:31194400-31211000	Strong transcription	Fetal Intestine Large	intestine
25	chr16:31194600-31196600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr16:31194600-31196600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr16:31194600-31196800	Strong transcription	Primary hematopoietic stem cells	blood
28	chr16:31194600-31196800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr16:31194600-31199000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr16:31194600-31207000	Strong transcription	Aorta	Aorta
31	chr16:31194600-31207800	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr16:31194600-31208400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr16:31194600-31208800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr16:31194600-31209000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr16:31194800-31198600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr16:31194800-31208000	Strong transcription	Brain Angular Gyrus	brain
37	chr16:31195000-31196400	Strong transcription	HSMM	muscle
38	chr16:31195000-31196600	Genic enhancers	Stomach Smooth Muscle	stomach
39	chr16:31195000-31208000	Strong transcription	Esophagus	oesophagus
40	chr16:31195000-31208200	Strong transcription	NHEK	skin
41	chr16:31195000-31208400	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr16:31195000-31208800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr16:31195000-31208800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr16:31195000-31208800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr16:31195000-31211000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr16:31195000-31211000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr16:31195200-31196400	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr16:31195200-31199400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr16:31195200-31206400	Strong transcription	Pancreatic Islets	Pancreatic Islet
50	chr16:31195200-31208000	Strong transcription	Fetal Kidney	kidney

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