Variant report

Variant	rs41741
Chromosome Location	chr7:116438511-116438512
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

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	7:116434729-116454408..7:116610596-116619447	H1-hESC	embryonic stem cell:	embryo
6	chr7:116431432..116434327-chr7:116437378..116438880,2	MCF-7	breast:
7	chr7:116437480..116439119-chr7:116441918..116444462,2	K562	blood:
8	7:116434729-116454408..7:116782481-116788433	GM12878	blood:
9	7:116093970-116105948..7:116434729-116454408	GM12878	blood:
10	7:115967532-115969617..7:116434729-116454408	H1-hESC	embryonic stem cell:	embryo
11	7:116245779-116258944..7:116434729-116454408	Hela-S3	cervix:
12	chr7:116435360..116437038-chr7:116438110..116441034,2	MCF-7	breast:
13	7:116434729-116454408..7:117326534-117332210	H1-hESC	embryonic stem cell:	embryo
14	7:116434729-116454408..7:116580605-116585719	Hela-S3	cervix:

No data

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

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10215153	0.82[ASW][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs11770163	1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1621	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193686	0.82[ASW][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.80[YRI][hapmap];0.94[ASN][1000 genomes]
rs41787	0.81[JPT][hapmap]
rs41789	0.81[JPT][hapmap]
rs438	0.81[JPT][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41741	KCND2	cis	parietal	SCAN
rs41741	MET	cis	Artery Aorta	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116421800-116444000	Weak transcription	Esophagus	oesophagus
2	chr7:116423000-116439000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:116423000-116442600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:116424000-116440800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:116424200-116440600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:116424200-116445400	Weak transcription	Left Ventricle	heart
7	chr7:116425000-116440800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:116426200-116440800	Weak transcription	HSMMtube	muscle
9	chr7:116427000-116440800	Weak transcription	NHDF-Ad	bronchial
10	chr7:116427400-116440200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:116427400-116445200	Weak transcription	Pancreas	Pancrea
12	chr7:116429600-116441200	Weak transcription	Fetal Lung	lung
13	chr7:116430800-116440000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr7:116432400-116439200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:116433200-116442400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr7:116433200-116442600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr7:116434800-116442200	Weak transcription	Brain Substantia Nigra	brain
18	chr7:116435000-116438600	Weak transcription	Colonic Mucosa	Colon
19	chr7:116435400-116439000	Strong transcription	Osteobl	bone
20	chr7:116435600-116438800	Strong transcription	HMEC	breast
21	chr7:116435800-116442400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr7:116436200-116438600	Genic enhancers	A549	lung
23	chr7:116436200-116442600	Weak transcription	HUVEC	blood vessel
24	chr7:116436200-116442800	Weak transcription	Aorta	Aorta
25	chr7:116436400-116439000	Genic enhancers	Muscle Satellite Cultured Cells	--
26	chr7:116436400-116439200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:116436400-116439800	Weak transcription	Liver	Liver
28	chr7:116436400-116440800	Weak transcription	NH-A	brain
29	chr7:116436600-116443800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr7:116436600-116445000	Enhancers	Hela-S3	cervix
31	chr7:116436800-116440600	Weak transcription	HepG2	liver
32	chr7:116436800-116442600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr7:116437000-116439200	Enhancers	Fetal Intestine Small	intestine
34	chr7:116437000-116440600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:116437000-116440800	Weak transcription	Placenta	Placenta
36	chr7:116437000-116441000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr7:116437000-116442200	Weak transcription	Fetal Muscle Leg	muscle
38	chr7:116437000-116444600	Weak transcription	Fetal Stomach	stomach
39	chr7:116437200-116438600	Genic enhancers	NHEK	skin
40	chr7:116437200-116439000	Enhancers	Stomach Mucosa	stomach
41	chr7:116437400-116438600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:116437400-116442000	Enhancers	Fetal Intestine Large	intestine
43	chr7:116437600-116438800	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr7:116437800-116438800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr7:116437800-116439000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:116437800-116439200	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr7:116438000-116438600	Enhancers	Adipose Nuclei	Adipose
48	chr7:116438000-116438600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr7:116438000-116438800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr7:116438000-116438800	Enhancers	Duodenum Mucosa	Duodenum

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