Variant report

Variant	rs42229
Chromosome Location	chr7:116442287-116442288
allele	C/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	chr7:116434861..116437169-chr7:116440116..116443011,2	K562	blood:
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	chr7:116437480..116439119-chr7:116441918..116444462,2	K562	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	7:116434729-116454408..7:117326534-117332210	H1-hESC	embryonic stem cell:	embryo
13	7:116434729-116454408..7:116580605-116585719	Hela-S3	cervix:
14	chr7:116441710..116444536-chr7:116449070..116450734,2	MCF-7	breast:

No data

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

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10435378	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs168686	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16945	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs183642	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs187437	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs193688	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2023748	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237717	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2299439	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35759345	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38859	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41735	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41736	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41737	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41738	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41739	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41743	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41744	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41746	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41747	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41748	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41749	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs42336	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs42374	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6566	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6947629	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6951311	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6978135	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116421800-116444000	Weak transcription	Esophagus	oesophagus
2	chr7:116423000-116442600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:116424200-116445400	Weak transcription	Left Ventricle	heart
4	chr7:116427400-116445200	Weak transcription	Pancreas	Pancrea
5	chr7:116433200-116442400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr7:116433200-116442600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr7:116435800-116442400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:116436200-116442600	Weak transcription	HUVEC	blood vessel
9	chr7:116436200-116442800	Weak transcription	Aorta	Aorta
10	chr7:116436600-116443800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr7:116436600-116445000	Enhancers	Hela-S3	cervix
12	chr7:116436800-116442600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr7:116437000-116444600	Weak transcription	Fetal Stomach	stomach
14	chr7:116438600-116442800	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:116438800-116442600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr7:116438800-116444600	Weak transcription	Colonic Mucosa	Colon
17	chr7:116438800-116448600	Weak transcription	Psoas Muscle	Psoas
18	chr7:116439800-116444600	Weak transcription	Small Intestine	intestine
19	chr7:116439800-116446000	Enhancers	Liver	Liver
20	chr7:116440000-116442400	Enhancers	Muscle Satellite Cultured Cells	--
21	chr7:116440200-116442400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr7:116440200-116443600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr7:116440200-116443600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:116440600-116443000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:116440600-116445400	Enhancers	HepG2	liver
26	chr7:116440800-116442600	Enhancers	HSMM	muscle
27	chr7:116440800-116442600	Enhancers	HSMMtube	muscle
28	chr7:116440800-116442600	Enhancers	NH-A	brain
29	chr7:116440800-116442600	Enhancers	NHDF-Ad	bronchial
30	chr7:116440800-116442600	Enhancers	Osteobl	bone
31	chr7:116440800-116443600	Enhancers	NHLF	lung
32	chr7:116440800-116443800	Flanking Active TSS	A549	lung
33	chr7:116440800-116445200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr7:116441000-116442600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:116441000-116444000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr7:116441000-116448400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr7:116441200-116442600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr7:116441400-116442600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr7:116441400-116442800	Weak transcription	Stomach Mucosa	stomach
40	chr7:116441400-116443600	Enhancers	Brain Cingulate Gyrus	brain
41	chr7:116441600-116442800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr7:116441800-116442800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr7:116441800-116443000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr7:116441800-116443400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:116441800-116443600	Enhancers	HMEC	breast
46	chr7:116441800-116443800	Enhancers	NHEK	skin
47	chr7:116441800-116444000	Enhancers	Placenta	Placenta
48	chr7:116442000-116442400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr7:116442000-116442400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:116442000-116442400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links