Variant report

Variant	rs41752
Chromosome Location	chr7:116450855-116450856
allele	A/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	EP300	chr7:116450269-116451289	HepG2	liver:	n/a	n/a
2	SMC3	chr7:116449331-116450879	Hela-S3	cervix:	n/a	chr7:116449932-116449946
3	POLR2A	chr7:116450597-116451296	HepG2	liver:	n/a	n/a
4	KAP1	chr7:116449699-116451068	HEK293	kidney:	n/a	n/a
5	FOXA1	chr7:116450204-116452038	HepG2	liver:	n/a	chr7:116451563-116451575
6	BHLHE40	chr7:116450466-116451159	HepG2	liver:	n/a	n/a
7	MXI1	chr7:116450411-116451302	HepG2	liver:	n/a	n/a
8	FOXA1	chr7:116450319-116451527	HepG2	liver:	n/a	n/a
9	FOSL2	chr7:116450794-116451160	HepG2	liver:	n/a	n/a
10	MAFF	chr7:116450318-116451229	HepG2	liver:	n/a	n/a
11	POLR2A	chr7:116450852-116451593	HepG2	liver:	n/a	n/a
12	BRCA1	chr7:116449737-116450902	Hela-S3	cervix:	n/a	n/a
13	FOXA2	chr7:116448392-116451986	HepG2	liver:	n/a	chr7:116451563-116451575
14	RXRA	chr7:116450786-116451207	HepG2	liver:	n/a	n/a
15	TCF12	chr7:116450112-116451050	ECC-1	luminal epithelium:	n/a	chr7:116450996-116451005
16	PBX3	chr7:116450270-116450948	SK-N-SH	brain:	n/a	n/a
17	RCOR1	chr7:116450459-116451209	HepG2	liver:	n/a	n/a
18	FOXA1	chr7:116450312-116451334	HepG2	liver:	n/a	n/a
19	KAP1	chr7:116449864-116451112	U2OS	brain:	n/a	n/a
20	MYBL2	chr7:116449437-116451469	HepG2	liver:	n/a	n/a
21	GATA3	chr7:116450283-116450992	SK-N-SH	brain:	n/a	chr7:116450936-116450952 chr7:116450939-116450949
22	MAX	chr7:116449801-116450887	Hela-S3	cervix:	n/a	n/a
23	JUND	chr7:116449720-116451033	Hela-S3	cervix:	n/a	chr7:116450001-116450011
24	ESR1	chr7:116450273-116450933	ECC-1	luminal epithelium:	n/a	chr7:116450513-116450530
25	FOXA1	chr7:116450311-116451317	HepG2	liver:	n/a	n/a
26	CTCF	chr7:116449129-116451186	SK-N-SH	brain:	n/a	chr7:116449931-116449947 chr7:116449925-116449946 chr7:116449930-116449948 chr7:116449935-116449943
27	EP300	chr7:116449825-116451054	ECC-1	luminal epithelium:	n/a	chr7:116449853-116449863
28	EP300	chr7:116450252-116451301	HepG2	liver:	n/a	n/a
29	NR2F2	chr7:116450390-116451010	MCF-7	breast:	n/a	n/a
30	HNF4A	chr7:116450820-116451220	HepG2	liver:	n/a	chr7:116451022-116451037
31	NFIC	chr7:116450244-116450918	ECC-1	luminal epithelium:	n/a	n/a
32	HNF4A	chr7:116450353-116451228	HepG2	liver:	n/a	chr7:116451022-116451037 chr7:116450619-116450637 chr7:116450620-116450635 chr7:116450586-116450598
33	TCF7L2	chr7:116449762-116451160	PANC-1	pancreas:	n/a	chr7:116450060-116450070
34	NR2F2	chr7:116450209-116451352	HepG2	liver:	n/a	n/a
35	ZNF217	chr7:116450475-116450893	MCF-7	breast:	n/a	n/a
36	MYBL2	chr7:116449276-116451322	HepG2	liver:	n/a	n/a
37	REST	chr7:116450800-116451290	HepG2	liver:	n/a	chr7:116451140-116451154
38	RFX5	chr7:116450442-116451139	HepG2	liver:	n/a	n/a
39	NFIC	chr7:116450189-116450992	ECC-1	luminal epithelium:	n/a	n/a
40	TCF12	chr7:116450235-116450927	SK-N-SH	brain:	n/a	n/a
41	EP300	chr7:116450349-116451249	HepG2	liver:	n/a	n/a
42	NFIC	chr7:116449183-116451629	HepG2	liver:	n/a	n/a
43	JUN	chr7:116449840-116451332	HepG2	liver:	n/a	chr7:116450001-116450011
44	CEBPB	chr7:116450277-116451149	HepG2	liver:	n/a	chr7:116450504-116450521 chr7:116450506-116450517 chr7:116450955-116450966 chr7:116450955-116450966
45	ARID3A	chr7:116449495-116451559	HepG2	liver:	n/a	chr7:116451391-116451407 chr7:116451392-116451408
46	HEY1	chr7:116450847-116451427	HepG2	liver:	n/a	n/a
47	MAFK	chr7:116450461-116451170	HepG2	liver:	n/a	n/a
48	TCF12	chr7:116449571-116451042	A549	lung:	n/a	chr7:116450996-116451005
49	RCOR1	chr7:116449822-116450900	Hela-S3	cervix:	n/a	n/a
50	TCF7L2	chr7:116450356-116451226	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:116339031-116340618..7:116434729-116454408	Hela-S3	cervix:
2	7:116071525-116078307..7:116434729-116454408	H1-hESC	embryonic stem cell:	embryo
3	7:116434729-116454408..7:117341506-117356953	Hela-S3	cervix:
4	7:116434729-116454408..7:117641436-117645830	GM12878	blood:
5	chr7:116449194..116452032-chr7:116500966..116504304,4	MCF-7	breast:
6	7:116434729-116454408..7:116610596-116619447	H1-hESC	embryonic stem cell:	embryo
7	7:116434729-116454408..7:116782481-116788433	GM12878	blood:
8	7:116093970-116105948..7:116434729-116454408	GM12878	blood:
9	7:115967532-115969617..7:116434729-116454408	H1-hESC	embryonic stem cell:	embryo
10	7:116245779-116258944..7:116434729-116454408	Hela-S3	cervix:
11	7:116434729-116454408..7:117326534-117332210	H1-hESC	embryonic stem cell:	embryo
12	7:116434729-116454408..7:116580605-116585719	Hela-S3	cervix:

Variant related genes	Relation type
CAPZA2	TF binding region
ENSG00000243243	Chromatin interaction
ENSG00000001626	Chromatin interaction
ENSG00000237813	Chromatin interaction
ENSG00000226367	Chromatin interaction
ENSG00000105976	Chromatin interaction
ENSG00000252672	Chromatin interaction
ENSG00000231210	Chromatin interaction
ENSG00000198898	Chromatin interaction
ENSG00000234826	Chromatin interaction
ENSG00000213050	Chromatin interaction
ENSG00000222150	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11766819	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41753	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41756	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41761	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41765	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41766	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41767	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41768	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41769	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41772	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41774	0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41775	0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41777	0.88[ASN][1000 genomes]
rs41780	0.88[ASN][1000 genomes]
rs41790	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs42337	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs42383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4730762	0.90[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56355906	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	nsv831107	chr7:116414734-116649466	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41752	CASP4	trans	parietal	SCAN
rs41752	CAV2	cis	lymphoblastoid	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116448600-116451000	Enhancers	Liver	Liver
2	chr7:116448600-116453200	Enhancers	Duodenum Mucosa	Duodenum
3	chr7:116448600-116453800	Enhancers	Fetal Intestine Small	intestine
4	chr7:116448600-116454000	Enhancers	Fetal Intestine Large	intestine
5	chr7:116449200-116451600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:116449200-116452000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr7:116449200-116453400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr7:116449200-116453400	Weak transcription	Pancreas	Pancrea
9	chr7:116449400-116451000	Weak transcription	Small Intestine	intestine
10	chr7:116449400-116451200	Enhancers	Fetal Lung	lung
11	chr7:116449400-116451200	Flanking Active TSS	A549	lung
12	chr7:116449400-116452000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:116449400-116452000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr7:116449400-116452800	Enhancers	Fetal Kidney	kidney
15	chr7:116449600-116451000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:116449600-116451000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr7:116449600-116452000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr7:116449600-116452600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr7:116449800-116452600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:116450000-116451200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:116450000-116451200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:116450000-116451200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr7:116450000-116451200	Enhancers	Placenta	Placenta
24	chr7:116450000-116451200	Enhancers	Osteobl	bone
25	chr7:116450000-116451800	Enhancers	Adipose Nuclei	Adipose
26	chr7:116450200-116451000	Weak transcription	Stomach Mucosa	stomach
27	chr7:116450400-116451200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:116450400-116451400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr7:116450400-116452200	Enhancers	Hela-S3	cervix
30	chr7:116450600-116451600	Active TSS	HepG2	liver
31	chr7:116450600-116452600	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr7:116450600-116453000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:116450600-116453200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr7:116450600-116453800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr7:116450800-116451800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr7:116450800-116453000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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