Variant report

Variant	rs440342
Chromosome Location	chr5:94977508-94977509
allele	C/G
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	FOXA1	chr5:94977425-94977821	T-47D	breast:	n/a	n/a
2	NR3C1	chr5:94977484-94977869	A549	lung:	n/a	n/a
3	FOXA1	chr5:94977461-94977844	HepG2	liver:	n/a	n/a
4	FOXA1	chr5:94977420-94977846	HepG2	liver:	n/a	n/a
5	JUND	chr5:94977481-94977899	HepG2	liver:	n/a	chr5:94977721-94977730
6	JUND	chr5:94977431-94977893	K562	blood:	n/a	chr5:94977721-94977730
7	POLR2A	chr5:94977381-94977581	HepG2	liver:	n/a	n/a
8	TBL1XR1	chr5:94977507-94977518	K562	blood:	n/a	n/a
9	GATA3	chr5:94977434-94977961	T-47D	breast:	n/a	chr5:94977564-94977572 chr5:94977454-94977462
10	NR3C1	chr5:94977480-94977817	A549	lung:	n/a	chr5:94977482-94977499
11	FOXA2	chr5:94977488-94977779	HepG2	liver:	n/a	n/a
12	NR3C1	chr5:94977496-94977869	A549	lung:	n/a	n/a
13	GATA3	chr5:94977448-94978069	MCF-7	breast:	n/a	chr5:94977564-94977572 chr5:94977454-94977462
14	GATA3	chr5:94977439-94977924	T-47D	breast:	n/a	chr5:94977564-94977572 chr5:94977454-94977462
15	SIN3AK20	chr5:94977282-94978035	MCF-7	breast:	n/a	n/a
16	TBP	chr5:94977486-94977789	HepG2	liver:	n/a	n/a
17	ARID3A	chr5:94977503-94977803	HepG2	liver:	n/a	n/a
18	MAFK	chr5:94977491-94977844	HepG2	liver:	n/a	chr5:94977668-94977683

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:94893117..94894866-chr5:94974664..94977618,2	K562	blood:
2	chr5:94977116..95012475-chr5:95055682..95079552,215	K562	blood:

Variant related genes	Relation type
RFESD	TF binding region
ENSG00000250240	Chromatin interaction
ENSG00000164292	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10063774	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13166682	1.00[CHB][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs13172592	0.98[ASN][1000 genomes]
rs13179768	0.97[ASN][1000 genomes]
rs150548	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs150549	0.95[CHB][hapmap];0.93[ASN][1000 genomes]
rs150550	0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs213507	0.95[ASN][1000 genomes]
rs213508	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213509	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213510	0.95[CHB][hapmap];0.93[ASN][1000 genomes]
rs213511	0.93[ASN][1000 genomes]
rs213512	0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[ASN][1000 genomes]
rs213880	0.81[CEU][hapmap];0.94[CHB][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs213885	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs213887	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213888	0.99[ASN][1000 genomes]
rs411817	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs412026	0.91[CHB][hapmap];0.93[CHD][hapmap];0.92[ASN][1000 genomes]
rs4869245	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.96[ASN][1000 genomes]
rs6865873	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6890832	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[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	nsv598955	chr5:94903453-95136019	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv598960	chr5:94975592-94988482	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs440342	RHOBTB3	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94968200-94979800	Weak transcription	Primary T cells from cord blood	blood
2	chr5:94974800-94979800	Weak transcription	GM12878-XiMat	blood
3	chr5:94975200-94979200	Enhancers	Pancreas	Pancrea
4	chr5:94976000-94982400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:94976600-94978200	Enhancers	Fetal Intestine Small	intestine
6	chr5:94976600-94978600	Enhancers	Fetal Intestine Large	intestine
7	chr5:94976800-94978200	Enhancers	Stomach Mucosa	stomach
8	chr5:94976800-94978400	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr5:94976800-94982200	Enhancers	Liver	Liver
10	chr5:94977000-94977600	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr5:94977000-94977800	Enhancers	Duodenum Mucosa	Duodenum
12	chr5:94977200-94977800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr5:94977200-94978000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:94977400-94977600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:94977400-94977600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:94977400-94977600	Enhancers	Gastric	stomach
17	chr5:94977400-94977600	Enhancers	Left Ventricle	heart
18	chr5:94977400-94977600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr5:94977400-94977600	Enhancers	Right Atrium	heart
20	chr5:94977400-94977600	Enhancers	HSMM	muscle
21	chr5:94977400-94977600	Enhancers	NHLF	lung
22	chr5:94977400-94977800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:94977400-94977800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:94977400-94977800	Flanking Active TSS	HepG2	liver
25	chr5:94977400-94978000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr5:94977400-94978200	Enhancers	K562	blood
27	chr5:94977400-94978400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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