Variant report

Variant	rs41750
Chromosome Location	chr7:116449000-116449001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr7:116448392-116451986	HepG2	liver:	n/a	chr7:116451563-116451575
2	RAD21	chr7:116448989-116450409	SK-N-SH	brain:	n/a	chr7:116449928-116449947
3	SMC3	chr7:116448418-116450335	SK-N-SH	brain:	n/a	chr7:116449932-116449946

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:116237088..116239163-chr7:116448010..116450403,3	K562	blood:
2	7:116339031-116340618..7:116434729-116454408	Hela-S3	cervix:
3	7:116071525-116078307..7:116434729-116454408	H1-hESC	embryonic stem cell:	embryo
4	chr7:116312036..116314941-chr7:116447219..116449000,2	MCF-7	breast:
5	7:116434729-116454408..7:117341506-117356953	Hela-S3	cervix:
6	7:116434729-116454408..7:117641436-117645830	GM12878	blood:
7	7:116434729-116454408..7:116610596-116619447	H1-hESC	embryonic stem cell:	embryo
8	chr7:116238085..116239028-chr7:116448998..116450414,5	MCF-7	breast:
9	7:116434729-116454408..7:116782481-116788433	GM12878	blood:
10	chr7:116448533..116450552-chr7:116591389..116593850,2	MCF-7	breast:
11	7:116093970-116105948..7:116434729-116454408	GM12878	blood:
12	7:115967532-115969617..7:116434729-116454408	H1-hESC	embryonic stem cell:	embryo
13	7:116245779-116258944..7:116434729-116454408	Hela-S3	cervix:
14	7:116434729-116454408..7:117326534-117332210	H1-hESC	embryonic stem cell:	embryo
15	7:116434729-116454408..7:116580605-116585719	Hela-S3	cervix:

No data

Variant related genes	Relation type
CAPZA2	TF binding region
ENSG00000237813	Chromatin interaction
ENSG00000001626	Chromatin interaction
ENSG00000252672	Chromatin interaction
ENSG00000222150	Chromatin interaction
ENSG00000234826	Chromatin interaction
ENSG00000105976	Chromatin interaction
ENSG00000243243	Chromatin interaction
ENSG00000004866	Chromatin interaction
ENSG00000226367	Chromatin interaction
ENSG00000231210	Chromatin interaction
ENSG00000213050	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10215153	0.80[YRI][hapmap]
rs1356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs193686	0.80[YRI][hapmap]
rs28167	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28896	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41754	0.84[CEU][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs41758	0.84[CEU][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs41770	0.85[EUR][1000 genomes]
rs41773	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41779	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41781	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41783	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41784	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41787	0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs41789	0.88[CHB][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.82[ASN][1000 genomes]
rs41791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41792	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs42338	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs42375	0.82[ASN][1000 genomes]
rs438	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs7803820	0.80[CEU][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41750	CTTNBP2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116443000-116449400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr7:116443400-116449200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr7:116443600-116449600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:116443600-116449600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:116443600-116450000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:116444000-116449000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:116445400-116449400	Weak transcription	NHEK	skin
8	chr7:116445400-116450000	Weak transcription	Adipose Nuclei	Adipose
9	chr7:116445600-116449600	Weak transcription	NHDF-Ad	bronchial
10	chr7:116445600-116450000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:116445600-116450000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr7:116445600-116450000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:116445600-116450000	Weak transcription	Placenta	Placenta
14	chr7:116445600-116450400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:116445800-116449400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:116445800-116449600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:116445800-116449600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr7:116446000-116449600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:116446200-116449600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr7:116446200-116450000	Weak transcription	Osteobl	bone
21	chr7:116446400-116449400	Enhancers	A549	lung
22	chr7:116446400-116449400	Enhancers	HepG2	liver
23	chr7:116446600-116449400	Weak transcription	Brain Angular Gyrus	brain
24	chr7:116446600-116450000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr7:116447200-116449400	Weak transcription	Fetal Lung	lung
26	chr7:116448400-116449400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:116448400-116450000	Enhancers	Hela-S3	cervix
28	chr7:116448400-116450800	Enhancers	HUVEC	blood vessel
29	chr7:116448600-116449200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:116448600-116449200	Enhancers	Pancreas	Pancrea
31	chr7:116448600-116449400	Enhancers	Gastric	stomach
32	chr7:116448600-116449400	Enhancers	Small Intestine	intestine
33	chr7:116448600-116449600	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr7:116448600-116449600	Enhancers	Stomach Mucosa	stomach
35	chr7:116448600-116450000	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr7:116448600-116450200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr7:116448600-116450600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr7:116448600-116451000	Enhancers	Liver	Liver
39	chr7:116448600-116453200	Enhancers	Duodenum Mucosa	Duodenum
40	chr7:116448600-116453800	Enhancers	Fetal Intestine Small	intestine
41	chr7:116448600-116454000	Enhancers	Fetal Intestine Large	intestine
42	chr7:116448800-116449200	Weak transcription	Fetal Stomach	stomach
43	chr7:116448800-116450000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr7:116448800-116450000	Weak transcription	Fetal Heart	heart
45	chr7:116448800-116450000	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr7:116449000-116449800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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