Variant report

Variant	rs17241389
Chromosome Location	chr7:83764309-83764310
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10488268	0.83[MEX][hapmap]
rs1156053	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1156054	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12707613	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12707614	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12707618	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12707620	0.81[AMR][1000 genomes]
rs13228082	0.87[MEX][hapmap]
rs13228833	0.95[MEX][hapmap];0.85[AMR][1000 genomes]
rs13233962	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17241955	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17242340	0.87[MEX][hapmap]
rs17298417	0.83[MEX][hapmap]
rs17300760	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1990044	0.88[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1990045	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2040871	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2301891	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2372031	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2372032	0.92[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2372035	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3029	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757624	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3779443	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3779444	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3801616	0.87[MEX][hapmap]
rs3801629	0.91[MEX][hapmap]
rs3801634	0.80[AMR][1000 genomes]
rs3801636	0.80[AMR][1000 genomes]
rs3801637	0.80[AMR][1000 genomes]
rs3801641	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3801642	0.92[CEU][hapmap];0.95[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3801644	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3801645	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3801649	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3801650	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3823911	0.87[MEX][hapmap]
rs41441447	0.87[MEX][hapmap]
rs4732544	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55679601	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6957333	0.84[AMR][1000 genomes]
rs6965990	0.87[MEX][hapmap]
rs723997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs727650	0.83[MEX][hapmap]
rs727651	0.82[MEX][hapmap]
rs757682	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs764116	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs764117	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7789342	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804363	0.87[MEX][hapmap]
rs917089	0.87[MEX][hapmap]
rs917090	0.91[MEX][hapmap]
rs933340	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs995866	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529344	chr7:83714286-84592857	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv888629	chr7:83722691-83896025	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1017884	chr7:83724138-83972995	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538995	chr7:83724138-83972995	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17241389	TCHP	trans	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83745000-83769400	Weak transcription	Fetal Stomach	stomach
2	chr7:83752600-83769600	Weak transcription	A549	lung
3	chr7:83753800-83766800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:83753800-83766800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:83753800-83768000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:83753800-83768200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr7:83753800-83769600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr7:83753800-83770800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:83754000-83767400	Weak transcription	NHLF	lung
10	chr7:83754000-83767800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:83754000-83772200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:83754000-83774200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:83755000-83768800	Weak transcription	Colon Smooth Muscle	Colon
14	chr7:83758600-83765400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr7:83761000-83768600	Weak transcription	Fetal Lung	lung
16	chr7:83761000-83775200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr7:83762200-83764400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:83762400-83764400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr7:83763000-83764600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr7:83763400-83764400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:83763400-83764400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:83763400-83764400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr7:83763400-83764400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr7:83764000-83765000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:83764000-83765800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:83764200-83765600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:83764200-83767800	Weak transcription	NHDF-Ad	bronchial
28	chr7:83764200-83771800	Weak transcription	Stomach Smooth Muscle	stomach

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