Variant report

Variant	rs723997
Chromosome Location	chr7:83775796-83775797
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1156053	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1156054	0.88[EUR][1000 genomes]
rs12707613	0.88[EUR][1000 genomes]
rs12707614	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12707618	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13228833	0.91[MEX][hapmap]
rs13233962	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17158679	0.95[YRI][hapmap]
rs17241389	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]
rs17241955	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17242340	0.92[MEX][hapmap]
rs17300760	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1990044	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs1990045	0.87[EUR][1000 genomes]
rs2040871	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2301891	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2372031	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2372032	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs2372035	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3029	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3757624	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3779443	0.88[EUR][1000 genomes]
rs3779444	0.88[EUR][1000 genomes]
rs3801629	0.83[MEX][hapmap]
rs3801641	0.88[EUR][1000 genomes]
rs3801642	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs3801644	0.88[EUR][1000 genomes]
rs3801645	0.88[EUR][1000 genomes]
rs3801649	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3801650	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4732544	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55679601	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs757682	0.88[EUR][1000 genomes]
rs764116	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs764117	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7789342	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs917090	0.83[MEX][hapmap]
rs933340	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs995866	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.84[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
rs723997	TCHP	trans	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83767000-83776800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:83770800-83795000	Weak transcription	NHDF-Ad	bronchial
3	chr7:83771800-83777800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:83772000-83776200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr7:83772000-83777200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr7:83773000-83779400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:83773200-83779000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:83773400-83775800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:83774000-83776800	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr7:83774000-83778600	Enhancers	Colon Smooth Muscle	Colon
11	chr7:83774200-83775800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr7:83774200-83778000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:83774200-83778000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:83774600-83776800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr7:83774600-83777800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr7:83774600-83777800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr7:83774600-83777800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr7:83774600-83778000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr7:83775000-83775800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:83775200-83776000	Enhancers	Fetal Lung	lung
21	chr7:83775200-83776600	Enhancers	Fetal Heart	heart
22	chr7:83775200-83777000	Enhancers	NHLF	lung
23	chr7:83775400-83775800	Active TSS	A549	lung
24	chr7:83775400-83778800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:83775400-83791600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:83775600-83776200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr7:83775600-83776400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:83775600-83777400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:83775600-83778000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr7:83775600-83778600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr7:83775600-83779200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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