Variant report

Variant	rs3801656
Chromosome Location	chr7:83754013-83754014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:83743073..83745524-chr7:83752305..83754687,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10230974	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10231580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10232605	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10244779	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10257628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10263183	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10277194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10278542	0.93[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10282129	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10488270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10488271	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11769574	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11773308	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12707621	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13222995	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];0.95[ASN][1000 genomes]
rs13228652	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13246393	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1541410	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs17158648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17158650	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17158668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17158671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17301441	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2040873	0.83[EUR][1000 genomes]
rs2040874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2158567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2189851	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2214665	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2301892	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2372034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34018474	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34443324	0.89[ASN][1000 genomes]
rs34449541	0.89[ASN][1000 genomes]
rs34805696	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35789545	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3801653	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];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4461845	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6959163	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7778244	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7780521	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7781126	0.88[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs7791361	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7794876	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7811829	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[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:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83734400-83762800	Weak transcription	Fetal Muscle Leg	muscle
2	chr7:83743000-83756400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:83745000-83769400	Weak transcription	Fetal Stomach	stomach
4	chr7:83752600-83769600	Weak transcription	A549	lung
5	chr7:83753600-83760600	Weak transcription	Fetal Lung	lung
6	chr7:83753800-83754200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:83753800-83754600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:83753800-83754600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:83753800-83754800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:83753800-83755200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr7:83753800-83756400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:83753800-83758000	Weak transcription	NHDF-Ad	bronchial
13	chr7:83753800-83759400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:83753800-83763400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr7:83753800-83763400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr7:83753800-83763400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:83753800-83766800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:83753800-83766800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr7:83753800-83768000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:83753800-83768200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr7:83753800-83769600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr7:83753800-83770800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr7:83754000-83754200	Enhancers	HUVEC	blood vessel
24	chr7:83754000-83754200	Enhancers	NH-A	brain
25	chr7:83754000-83754400	Weak transcription	Colon Smooth Muscle	Colon
26	chr7:83754000-83754800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:83754000-83754800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr7:83754000-83755600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:83754000-83763400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr7:83754000-83767400	Weak transcription	NHLF	lung
31	chr7:83754000-83767800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:83754000-83772200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr7:83754000-83774200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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