Variant report

Variant	rs41748
Chromosome Location	chr7:116446573-116446574
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr7:116446010-116446586	HepG2	liver:	n/a	n/a
2	FOXA1	chr7:116445810-116446607	HepG2	liver:	n/a	n/a
3	FOXA2	chr7:116444850-116446717	HepG2	liver:	n/a	n/a
4	NR2F2	chr7:116445164-116446576	HepG2	liver:	n/a	n/a
5	MYBL2	chr7:116445836-116446688	HepG2	liver:	n/a	n/a
6	NR2F2	chr7:116445981-116446574	HepG2	liver:	n/a	n/a
7	FOXA1	chr7:116445815-116446601	HepG2	liver:	n/a	n/a
8	NFIC	chr7:116445797-116446664	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:116442420..116444484-chr7:116446523..116448838,2	MCF-7	breast:
2	7:116339031-116340618..7:116434729-116454408	Hela-S3	cervix:
3	7:116071525-116078307..7:116434729-116454408	H1-hESC	embryonic stem cell:	embryo
4	7:116434729-116454408..7:117341506-117356953	Hela-S3	cervix:
5	7:116434729-116454408..7:117641436-117645830	GM12878	blood:
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:

No data

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

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10435378	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs168686	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16945	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs183642	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs187437	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs193688	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2023748	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2237717	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2299439	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35759345	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs38859	0.88[EUR][1000 genomes]
rs41735	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41736	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41737	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41738	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41739	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41743	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41744	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41746	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41747	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41749	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42229	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs42336	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs42374	0.96[AFR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6566	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6947629	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6951311	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6978135	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs41748	MET	cis	thalamus	BrainEAC
rs41748	MET	cis	intralobular white matter	BrainEAC
rs41748	MET	cis	putamen	BrainEAC
rs41748	MET	cis	brain	BrainEAC
rs41748	MET	cis	inferior olivary nucleus	BrainEAC

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116438800-116448600	Weak transcription	Psoas Muscle	Psoas
2	chr7:116441000-116448400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:116442400-116446800	Enhancers	Fetal Intestine Large	intestine
4	chr7:116442400-116446800	Enhancers	Fetal Intestine Small	intestine
5	chr7:116443000-116449400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr7:116443200-116448600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:116443400-116449200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr7:116443600-116449600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr7:116443600-116449600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:116443600-116450000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:116444000-116449000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:116444600-116446600	Enhancers	Brain Cingulate Gyrus	brain
13	chr7:116444600-116447200	Enhancers	Fetal Lung	lung
14	chr7:116445200-116446600	Enhancers	Brain Angular Gyrus	brain
15	chr7:116445400-116448600	Weak transcription	Fetal Stomach	stomach
16	chr7:116445400-116449400	Weak transcription	NHEK	skin
17	chr7:116445400-116450000	Weak transcription	Adipose Nuclei	Adipose
18	chr7:116445600-116446600	Enhancers	Hela-S3	cervix
19	chr7:116445600-116446800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:116445600-116448600	Weak transcription	Pancreas	Pancrea
21	chr7:116445600-116448600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr7:116445600-116448600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr7:116445600-116449600	Weak transcription	NHDF-Ad	bronchial
24	chr7:116445600-116450000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr7:116445600-116450000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr7:116445600-116450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:116445600-116450000	Weak transcription	Placenta	Placenta
28	chr7:116445600-116450400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:116445800-116447200	Enhancers	HUVEC	blood vessel
30	chr7:116445800-116449400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:116445800-116449600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:116445800-116449600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr7:116446000-116446800	Enhancers	Fetal Kidney	kidney
34	chr7:116446000-116449600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:116446200-116448400	Weak transcription	NHLF	lung
36	chr7:116446200-116449600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:116446200-116450000	Weak transcription	Osteobl	bone
38	chr7:116446400-116447200	Enhancers	Liver	Liver
39	chr7:116446400-116448600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr7:116446400-116448600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr7:116446400-116448600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr7:116446400-116448600	Weak transcription	Small Intestine	intestine
43	chr7:116446400-116448600	Weak transcription	Stomach Mucosa	stomach
44	chr7:116446400-116448800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr7:116446400-116449400	Enhancers	A549	lung
46	chr7:116446400-116449400	Enhancers	HepG2	liver

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