Variant report

Variant	rs41746
Chromosome Location	chr7:116443074-116443075
allele	A/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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 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	chr7:116442420..116444484-chr7:116446523..116448838,2	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	chr7:116437480..116439119-chr7:116441918..116444462,2	K562	blood:
9	7:116093970-116105948..7:116434729-116454408	GM12878	blood:
10	chr7:116311093..116312052-chr7:116442635..116443208,4	MCF-7	breast:
11	chr7:116311536..116312726-chr7:116442552..116443304,4	MCF-7	breast:
12	7:115967532-115969617..7:116434729-116454408	H1-hESC	embryonic stem cell:	embryo
13	7:116245779-116258944..7:116434729-116454408	Hela-S3	cervix:
14	chr7:115812797..115813710-chr7:116442637..116443182,2	K562	blood:
15	7:116434729-116454408..7:117326534-117332210	H1-hESC	embryonic stem cell:	embryo
16	7:116434729-116454408..7:116580605-116585719	Hela-S3	cervix:
17	chr7:116441710..116444536-chr7:116449070..116450734,2	MCF-7	breast:

No data

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

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10435378	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1049618	1.00[YRI][hapmap]
rs168686	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16945	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183642	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs187437	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs193688	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[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2023748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237717	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2299439	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2402118	0.84[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs35759345	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38848	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs38851	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs38854	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs38859	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs39748	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs41735	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41737	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41738	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41739	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41744	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41747	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41748	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41749	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41774	1.00[YRI][hapmap]
rs41775	1.00[YRI][hapmap]
rs42229	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs42336	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42374	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4730762	1.00[YRI][hapmap]
rs6566	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947629	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6951311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964449	1.00[YRI][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

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116421800-116444000	Weak transcription	Esophagus	oesophagus
2	chr7:116424200-116445400	Weak transcription	Left Ventricle	heart
3	chr7:116427400-116445200	Weak transcription	Pancreas	Pancrea
4	chr7:116436600-116443800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr7:116436600-116445000	Enhancers	Hela-S3	cervix
6	chr7:116437000-116444600	Weak transcription	Fetal Stomach	stomach
7	chr7:116438800-116444600	Weak transcription	Colonic Mucosa	Colon
8	chr7:116438800-116448600	Weak transcription	Psoas Muscle	Psoas
9	chr7:116439800-116444600	Weak transcription	Small Intestine	intestine
10	chr7:116439800-116446000	Enhancers	Liver	Liver
11	chr7:116440200-116443600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr7:116440200-116443600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:116440600-116445400	Enhancers	HepG2	liver
14	chr7:116440800-116443600	Enhancers	NHLF	lung
15	chr7:116440800-116443800	Flanking Active TSS	A549	lung
16	chr7:116440800-116445200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr7:116441000-116444000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:116441000-116448400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:116441400-116443600	Enhancers	Brain Cingulate Gyrus	brain
20	chr7:116441800-116443400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:116441800-116443600	Enhancers	HMEC	breast
22	chr7:116441800-116443800	Enhancers	NHEK	skin
23	chr7:116441800-116444000	Enhancers	Placenta	Placenta
24	chr7:116442200-116443200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:116442200-116443400	Enhancers	Fetal Lung	lung
26	chr7:116442200-116443600	Enhancers	Adipose Nuclei	Adipose
27	chr7:116442200-116443800	Enhancers	Brain Substantia Nigra	brain
28	chr7:116442200-116445400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr7:116442200-116446400	Enhancers	Fetal Muscle Leg	muscle
30	chr7:116442400-116443400	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr7:116442400-116443400	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr7:116442400-116443600	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr7:116442400-116443600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:116442400-116443600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr7:116442400-116443600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr7:116442400-116443800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr7:116442400-116445200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr7:116442400-116446800	Enhancers	Fetal Intestine Large	intestine
39	chr7:116442400-116446800	Enhancers	Fetal Intestine Small	intestine
40	chr7:116442600-116443200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr7:116442600-116443200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr7:116442600-116443400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr7:116442600-116443400	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr7:116442600-116443400	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr7:116442600-116443400	Enhancers	Brain Anterior Caudate	brain
46	chr7:116442600-116443400	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr7:116442600-116443600	Enhancers	Brain Hippocampus Middle	brain
48	chr7:116442600-116443600	Enhancers	HUVEC	blood vessel
49	chr7:116442600-116446400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr7:116442800-116443200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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