Variant report

Variant	rs3029
Chromosome Location	chr7:83756418-83756419
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:83754771..83757226-chr7:83760360..83762151,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10488267	0.81[AMR][1000 genomes]
rs1156053	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1156054	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12707613	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12707614	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12707618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12707620	0.83[AMR][1000 genomes]
rs13224288	0.81[AMR][1000 genomes]
rs13228833	0.88[AMR][1000 genomes]
rs13233962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17241389	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]
rs17241955	0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17300760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1990043	0.81[AMR][1000 genomes]
rs1990044	0.96[CEU][hapmap];0.91[CHB][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1990045	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2040871	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2301891	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2372031	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2372032	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2372035	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2888221	0.81[AMR][1000 genomes]
rs34665905	0.81[AMR][1000 genomes]
rs3757624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3779443	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3779444	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3801629	0.81[AMR][1000 genomes]
rs3801630	0.81[AMR][1000 genomes]
rs3801632	0.81[AMR][1000 genomes]
rs3801633	0.81[AMR][1000 genomes]
rs3801634	0.83[AMR][1000 genomes]
rs3801636	0.83[AMR][1000 genomes]
rs3801637	0.83[AMR][1000 genomes]
rs3801641	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3801642	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3801643	0.81[AMR][1000 genomes]
rs3801644	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3801645	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3801649	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3801650	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4732541	0.81[AMR][1000 genomes]
rs4732544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55679601	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6957333	0.87[AMR][1000 genomes]
rs6970168	0.82[AMR][1000 genomes]
rs723997	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]
rs757682	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs764116	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs764117	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7789342	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7808725	0.81[AMR][1000 genomes]
rs7808859	0.81[AMR][1000 genomes]
rs917089	0.80[AMR][1000 genomes]
rs917090	0.81[AMR][1000 genomes]
rs933340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs995866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv994067	chr7:83749438-83759598	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83734400-83762800	Weak transcription	Fetal Muscle Leg	muscle
2	chr7:83745000-83769400	Weak transcription	Fetal Stomach	stomach
3	chr7:83752600-83769600	Weak transcription	A549	lung
4	chr7:83753600-83760600	Weak transcription	Fetal Lung	lung
5	chr7:83753800-83758000	Weak transcription	NHDF-Ad	bronchial
6	chr7:83753800-83759400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr7:83753800-83763400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr7:83753800-83763400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr7:83753800-83763400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:83753800-83766800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:83753800-83766800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:83753800-83768000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:83753800-83768200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr7:83753800-83769600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:83753800-83770800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:83754000-83763400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr7:83754000-83767400	Weak transcription	NHLF	lung
18	chr7:83754000-83767800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:83754000-83772200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr7:83754000-83774200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:83754800-83756800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr7:83754800-83763400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:83755000-83763400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr7:83755000-83768800	Weak transcription	Colon Smooth Muscle	Colon
25	chr7:83755200-83757200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr7:83755600-83756800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr7:83756200-83759000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr7:83756400-83756800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr7:83756400-83756800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr7:83756400-83759600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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