Variant report

Variant	rs72954810
Chromosome Location	chr4:152496421-152496422
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr4:152496414-152496436	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152452273..152454102-chr4:152495162..152497210,2	MCF-7	breast:
2	chr4:152493503..152497006-chr4:152497328..152500411,3	MCF-7	breast:

Variant related genes	Relation type
RN7SKP35	TF binding region
ENSG00000253019	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10002512	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10002750	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10010061	1.00[AMR][1000 genomes]
rs10014639	1.00[AMR][1000 genomes]
rs10015816	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10017489	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10020313	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10027105	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10032584	1.00[AMR][1000 genomes]
rs10034746	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10212987	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10213361	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10471071	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10471072	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13353741	1.00[AMR][1000 genomes]
rs13435896	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17027673	0.96[AFR][1000 genomes]
rs17027675	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17027703	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17027710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17027725	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17027738	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17027739	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17027742	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17027757	1.00[AMR][1000 genomes]
rs17027762	1.00[AMR][1000 genomes]
rs17027764	1.00[AMR][1000 genomes]
rs17027767	1.00[AMR][1000 genomes]
rs28404927	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28417352	1.00[AMR][1000 genomes]
rs28454065	1.00[AMR][1000 genomes]
rs28461656	1.00[AMR][1000 genomes]
rs28494961	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28539581	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28540596	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28558989	1.00[AMR][1000 genomes]
rs28591074	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28595853	1.00[AMR][1000 genomes]
rs28618192	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28634312	1.00[AMR][1000 genomes]
rs28656459	1.00[AMR][1000 genomes]
rs28722860	1.00[AMR][1000 genomes]
rs28788179	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28798801	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28822494	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28836879	0.98[AFR][1000 genomes]
rs28837860	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28884810	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57562339	1.00[AMR][1000 genomes]
rs61653326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72954898	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72956911	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72956926	1.00[AMR][1000 genomes]
rs72956927	1.00[AMR][1000 genomes]
rs9307882	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9307883	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9307884	1.00[AMR][1000 genomes]
rs9307885	1.00[AMR][1000 genomes]
rs9683731	1.00[AMR][1000 genomes]
rs9994720	1.00[AMR][1000 genomes]
rs9997778	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1025192	chr4:152202627-152498890	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv537307	chr4:152202627-152498890	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv880624	chr4:152280646-152549112	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv881342	chr4:152363772-152560449	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv830114	chr4:152401288-152548606	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152476600-152526600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:152484800-152518600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:152485600-152509600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:152485800-152498800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr4:152491200-152519000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:152491400-152497600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:152494400-152496800	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr4:152494800-152496800	Enhancers	Duodenum Mucosa	Duodenum
9	chr4:152495400-152496600	Weak transcription	Esophagus	oesophagus
10	chr4:152495400-152497600	Weak transcription	Spleen	Spleen
11	chr4:152495400-152497600	Enhancers	NHEK	skin
12	chr4:152495400-152503400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:152496000-152497600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:152496200-152496800	Enhancers	Fetal Intestine Large	intestine
15	chr4:152496200-152496800	Enhancers	Fetal Intestine Small	intestine
16	chr4:152496200-152497200	Enhancers	HMEC	breast
17	chr4:152496400-152496600	Enhancers	Gastric	stomach
18	chr4:152496400-152496800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr4:152496400-152496800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:152496400-152496800	Enhancers	Colonic Mucosa	Colon
21	chr4:152496400-152496800	Enhancers	Pancreas	Pancrea
22	chr4:152496400-152496800	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr4:152496400-152496800	Enhancers	Stomach Mucosa	stomach
24	chr4:152496400-152497000	Enhancers	Psoas Muscle	Psoas
25	chr4:152496400-152497000	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr4:152496400-152497200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:152496400-152497200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr4:152496400-152497600	Enhancers	Left Ventricle	heart

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