Variant report

Variant	rs11945232
Chromosome Location	chr4:88342369-88342370
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:88342245-88342669	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr4:88341808-88344299	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:88342319-88342616	K562	blood:	n/a	n/a
4	POLR2A	chr4:88341803-88342727	K562	blood:	n/a	n/a
5	MAX	chr4:88342367-88342544	H1-hESC	embryonic stem cell:	n/a	n/a
6	CEBPB	chr4:88342236-88342439	HepG2	liver:	n/a	n/a
7	POLR2A	chr4:88341921-88342844	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr4:88342287-88342418	HepG2	liver:	n/a	n/a
9	POLR2A	chr4:88342052-88344383	GM12891	blood:	n/a	n/a
10	POLR2A	chr4:88342303-88344277	GM18505	blood:	n/a	n/a
11	POLR2A	chr4:88342187-88344305	PFSK-1	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:88310667..88314164-chr4:88342247..88345345,4	K562	blood:
2	chr4:88341987..88343662-chr4:88383872..88386006,2	MCF-7	breast:
3	chr4:88340563..88342774-chr4:88344260..88346848,4	MCF-7	breast:
4	chr4:88340622..88342394-chr4:88382444..88384320,2	MCF-7	breast:
5	chr4:88341784..88343437-chr4:88384944..88387219,2	K562	blood:
6	chr4:88333084..88334930-chr4:88342115..88343742,2	MCF-7	breast:
7	chr4:88339085..88341655-chr4:88342092..88343723,2	MCF-7	breast:
8	chr4:88309813..88313902-chr4:88342245..88346379,5	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSD17B11-2	chr4:88341428-88343734	NONHSAT097311

No data

Variant related genes	Relation type
NUDT9	TF binding region
ENSG00000272856	Chromatin interaction
ENSG00000198189	Chromatin interaction
ENSG00000251716	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10010988	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10025902	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10027786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10032597	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11937770	0.86[YRI][hapmap]
rs13103927	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13113575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13138404	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13138636	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13150578	0.93[EUR][1000 genomes]
rs28372775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28406846	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28502849	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28609242	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28630962	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28701008	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28736552	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34549877	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35322242	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35371368	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4314250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6816224	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6827817	0.82[GIH][hapmap]
rs6839314	0.84[YRI][hapmap]
rs6854710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7659182	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11945232	HSD17B13	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88329600-88342600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:88334600-88342800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:88339400-88343000	Enhancers	Fetal Intestine Large	intestine
4	chr4:88340000-88343000	Enhancers	Fetal Intestine Small	intestine
5	chr4:88340000-88343000	Enhancers	Pancreas	Pancrea
6	chr4:88340400-88343000	Enhancers	Duodenum Mucosa	Duodenum
7	chr4:88340600-88342600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr4:88340600-88342600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr4:88340800-88342400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr4:88340800-88342400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr4:88340800-88342600	Enhancers	H1 Cell Line	embryonic stem cell
12	chr4:88340800-88342600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr4:88340800-88342600	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr4:88340800-88342600	Enhancers	Fetal Kidney	kidney
15	chr4:88340800-88342800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:88340800-88343000	Weak transcription	Colonic Mucosa	Colon
17	chr4:88340800-88343200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:88340800-88343200	Weak transcription	Gastric	stomach
19	chr4:88341000-88343000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr4:88341200-88342400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr4:88341200-88342400	Flanking Active TSS	HepG2	liver
22	chr4:88341200-88342800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr4:88341200-88343000	Weak transcription	Right Atrium	heart
24	chr4:88341400-88342400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:88341400-88342800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr4:88341400-88343000	Weak transcription	HUVEC	blood vessel
27	chr4:88341400-88343400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr4:88341600-88342600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:88341600-88342600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:88341600-88342800	Weak transcription	Psoas Muscle	Psoas
31	chr4:88341600-88343000	Weak transcription	NH-A	brain
32	chr4:88341800-88342800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:88341800-88343200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr4:88341800-88343200	Weak transcription	Small Intestine	intestine
35	chr4:88342000-88342600	Enhancers	GM12878-XiMat	blood
36	chr4:88342000-88343000	Weak transcription	Stomach Mucosa	stomach
37	chr4:88342200-88343000	Weak transcription	A549	lung
38	chr4:88342200-88343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr4:88342200-88343400	Flanking Active TSS	Liver	Liver

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