Variant report

Variant	rs9991367
Chromosome Location	chr4:110894301-110894302
allele	C/T
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	FOXA2	chr4:110894227-110894646	HepG2	liver:	n/a	n/a
2	CTCF	chr4:110894293-110894319	MCF-7	breast:	n/a	n/a
3	FOXA1	chr4:110894171-110894614	HepG2	liver:	n/a	n/a
4	FOXA1	chr4:110894301-110895282	HepG2	liver:	n/a	n/a
5	CTCF	chr4:110894220-110894370	Caco-2	colon:	n/a	chr4:110894316-110894329
6	CTCF	chr4:110894160-110894310	WERI-Rb-1	eye:	n/a	n/a
7	CTCF	chr4:110894257-110894314	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr4:110894240-110894390	Caco-2	colon:	n/a	chr4:110894316-110894329

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110888945..110892290-chr4:110892815..110895828,3	MCF-7	breast:

Variant related genes	Relation type
EGF	TF binding region
ENSG00000138798	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs10857004	1.00[CEU][hapmap]
rs11098060	0.88[CEU][hapmap]
rs11568943	0.88[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[ASN][1000 genomes]
rs11568978	0.91[AMR][1000 genomes]
rs11569008	0.94[AFR][1000 genomes]
rs11569017	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11569019	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11569020	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11569104	1.00[CEU][hapmap]
rs11569121	0.88[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap]
rs11569126	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs2074392	1.00[CEU][hapmap]
rs2237042	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs2237054	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2250724	0.94[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs2255355	0.93[TSI][hapmap]
rs2298982	0.87[TSI][hapmap]
rs2298986	0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2298996	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2299001	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap]
rs35860692	0.82[ASN][1000 genomes]
rs3733625	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs3733626	1.00[CEU][hapmap]
rs3756261	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs3796947	0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs6823529	0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs6825106	1.00[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs730598	0.94[JPT][hapmap]
rs7661968	0.93[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs7670908	0.90[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs881841	0.96[EUR][1000 genomes]
rs971695	1.00[CEU][hapmap]
rs971696	1.00[CEU][hapmap]
rs9995637	0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530156	chr4:110721397-110911297	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9991367	COL25A1	cis	brain	seeQTL
rs9991367	LRIT3	cis	brain	seeQTL
rs9991367	GAS7	trans	brain	seeQTL
rs9991367	C7orf58	trans	brain	seeQTL
rs9991367	ABCA2	trans	brain	seeQTL
rs9991367	NOTUM	trans	brain	seeQTL
rs9991367	RSPRY1	trans	brain	seeQTL
rs9991367	ENPEP	cis	brain	seeQTL
rs9991367	SGTA	trans	brain	seeQTL
rs9991367	PITX2	cis	brain	seeQTL
rs9991367	TACSTD2	trans	brain	seeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110860600-110906600	Weak transcription	Psoas Muscle	Psoas
2	chr4:110875600-110909800	Weak transcription	Pancreas	Pancrea
3	chr4:110885800-110897200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:110885800-110909800	Weak transcription	Left Ventricle	heart
5	chr4:110890200-110894400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:110890400-110900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:110891200-110900000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:110891600-110895400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr4:110891600-110896400	Weak transcription	Spleen	Spleen
10	chr4:110891800-110900000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:110892800-110894400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr4:110893000-110894400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr4:110893200-110894400	Enhancers	HSMMtube	muscle
14	chr4:110893400-110894600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr4:110893600-110894400	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr4:110893600-110894800	Enhancers	H1 Cell Line	embryonic stem cell
17	chr4:110893600-110894800	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr4:110893600-110895000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr4:110893600-110895000	Enhancers	Fetal Intestine Small	intestine
20	chr4:110893800-110894600	Enhancers	Fetal Muscle Leg	muscle
21	chr4:110893800-110895000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:110893800-110895000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:110893800-110909600	Weak transcription	Fetal Heart	heart
24	chr4:110894000-110894400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr4:110894000-110894400	Enhancers	H9 Cell Line	embryonic stem cell
26	chr4:110894000-110894400	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr4:110894000-110894800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:110894000-110894800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr4:110894000-110894800	Enhancers	Duodenum Mucosa	Duodenum
30	chr4:110894000-110895600	Enhancers	Fetal Intestine Large	intestine
31	chr4:110894200-110894600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr4:110894200-110894600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:110894200-110894600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr4:110894200-110894800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr4:110894200-110894800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:110894200-110894800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:110894200-110894800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr4:110894200-110894800	Flanking Active TSS	HepG2	liver

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