Variant report

Variant	rs984458
Chromosome Location	chr4:148403549-148403550
allele	C/T
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	FOS	chr4:148403331-148403879	MCF10A-Er-Src	breast:	n/a	chr4:148403388-148403395
2	STAT3	chr4:148403359-148403876	MCF10A-Er-Src	breast:	n/a	chr4:148403659-148403668 chr4:148403656-148403670 chr4:148403657-148403668 chr4:148403658-148403667 chr4:148403653-148403673
3	FOS	chr4:148403363-148403836	MCF10A-Er-Src	breast:	n/a	chr4:148403388-148403395
4	STAT3	chr4:148403196-148403886	MCF10A-Er-Src	breast:	n/a	chr4:148403659-148403668 chr4:148403656-148403670 chr4:148403657-148403668 chr4:148403658-148403667 chr4:148403653-148403673
5	STAT3	chr4:148403183-148403886	MCF10A-Er-Src	breast:	n/a	chr4:148403659-148403668 chr4:148403656-148403670 chr4:148403657-148403668 chr4:148403658-148403667 chr4:148403653-148403673
6	FOS	chr4:148403503-148403755	MCF10A-Er-Src	breast:	n/a	n/a
7	MYC	chr4:148403520-148403824	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr4:148403413-148403901	MCF10A-Er-Src	breast:	n/a	chr4:148403659-148403668 chr4:148403656-148403670 chr4:148403657-148403668 chr4:148403658-148403667 chr4:148403653-148403673
9	STAT3	chr4:148403544-148403749	MCF10A-Er-Src	breast:	n/a	chr4:148403659-148403668 chr4:148403656-148403670 chr4:148403657-148403668 chr4:148403658-148403667 chr4:148403653-148403673
10	FOS	chr4:148403274-148403880	MCF10A-Er-Src	breast:	n/a	chr4:148403388-148403395

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:148398530..148400390-chr4:148402721..148404279,2	MCF-7	breast:
2	chr4:148400285..148404582-chr4:148404756..148408817,4	K562	blood:

Variant related genes	Relation type
EDNRA	TF binding region
ENSG00000151617	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10011966	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10024834	0.95[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10305860	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10305862	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100963	0.88[ASN][1000 genomes]
rs11722942	0.87[ASN][1000 genomes]
rs11727337	0.87[ASN][1000 genomes]
rs11727397	0.87[ASN][1000 genomes]
rs11730985	0.87[ASN][1000 genomes]
rs11731096	0.83[ASN][1000 genomes]
rs11731097	0.83[ASN][1000 genomes]
rs11731134	0.87[ASN][1000 genomes]
rs12509416	0.90[ASN][1000 genomes]
rs12642328	0.88[ASN][1000 genomes]
rs13112065	0.87[ASN][1000 genomes]
rs13127894	0.86[ASN][1000 genomes]
rs13138887	0.82[ASN][1000 genomes]
rs13143677	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13144507	0.89[ASN][1000 genomes]
rs1366688	0.86[ASN][1000 genomes]
rs1400554	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1400558	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1400559	0.87[ASN][1000 genomes]
rs1400560	0.87[ASN][1000 genomes]
rs1517134	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1517138	0.87[ASN][1000 genomes]
rs1517139	0.87[ASN][1000 genomes]
rs17474816	0.95[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17474823	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1801708	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1949375	0.87[ASN][1000 genomes]
rs1996373	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1996374	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2063936	0.87[ASN][1000 genomes]
rs34256803	0.88[ASN][1000 genomes]
rs35686091	0.88[ASN][1000 genomes]
rs4631019	0.85[ASN][1000 genomes]
rs4835081	0.87[ASN][1000 genomes]
rs4835083	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835084	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835086	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4835401	0.87[ASN][1000 genomes]
rs4835405	0.87[ASN][1000 genomes]
rs4835407	0.87[ASN][1000 genomes]
rs4835410	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56015601	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57886575	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6537479	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6537480	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6537482	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6537483	0.95[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6537484	0.81[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs6810637	0.80[ASN][1000 genomes]
rs6817469	0.85[ASN][1000 genomes]
rs6819740	0.95[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6820938	0.98[ASN][1000 genomes]
rs6823537	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835512	0.81[ASN][1000 genomes]
rs6840108	0.85[ASN][1000 genomes]
rs6840756	0.95[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6840784	0.86[ASN][1000 genomes]
rs6848108	0.95[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6853791	0.80[ASN][1000 genomes]
rs6855875	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs702757	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655670	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7659823	0.98[ASN][1000 genomes]
rs7663891	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308218	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs952402	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959600	0.87[ASN][1000 genomes]
rs984457	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991584	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830109	chr4:148295061-148468605	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148401200-148404000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
2	chr4:148401400-148404400	Active TSS	Right Ventricle	heart
3	chr4:148401400-148404600	Active TSS	Fetal Kidney	kidney
4	chr4:148401600-148403600	Active TSS	Fetal Lung	lung
5	chr4:148401800-148404000	Bivalent/Poised TSS	Fetal Thymus	thymus
6	chr4:148401800-148404200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:148401800-148404200	Active TSS	Left Ventricle	heart
8	chr4:148401800-148404400	Active TSS	Ovary	ovary
9	chr4:148401800-148404600	Active TSS	Right Atrium	heart
10	chr4:148402000-148403600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:148402000-148403600	Active TSS	Stomach Smooth Muscle	stomach
12	chr4:148402000-148403800	Bivalent/Poised TSS	Psoas Muscle	Psoas
13	chr4:148402000-148403800	Active TSS	HSMMtube	muscle
14	chr4:148402000-148404000	Active TSS	Fetal Heart	heart
15	chr4:148402000-148404600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:148402400-148404200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:148402600-148403800	Flanking Active TSS	NHEK	skin
18	chr4:148402600-148404000	Flanking Active TSS	HMEC	breast
19	chr4:148402800-148403800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:148402800-148404000	Flanking Active TSS	NHDF-Ad	bronchial
21	chr4:148402800-148404000	Flanking Active TSS	NHLF	lung
22	chr4:148402800-148404200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
23	chr4:148402800-148404400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:148403000-148404000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
25	chr4:148403000-148404200	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr4:148403000-148404200	Active TSS	Fetal Stomach	stomach
27	chr4:148403000-148404400	Flanking Active TSS	NH-A	brain
28	chr4:148403000-148405600	Weak transcription	Spleen	Spleen
29	chr4:148403200-148403600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:148403200-148403600	Active TSS	Fetal Muscle Leg	muscle
31	chr4:148403200-148403800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:148403200-148404000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
33	chr4:148403200-148404000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
34	chr4:148403200-148404000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr4:148403200-148404000	Bivalent/Poised TSS	Fetal Brain Male	brain
36	chr4:148403200-148404000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
37	chr4:148403200-148404000	Weak transcription	Lung	lung
38	chr4:148403200-148404200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:148403200-148404200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:148403200-148404200	Active TSS	Gastric	stomach
41	chr4:148403200-148404200	Enhancers	Osteobl	bone
42	chr4:148403200-148404400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:148403200-148404400	Active TSS	Fetal Muscle Trunk	muscle
44	chr4:148403400-148403600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
45	chr4:148403400-148403600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
46	chr4:148403400-148403600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:148403400-148403800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
48	chr4:148403400-148403800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
49	chr4:148403400-148403800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:148403400-148403800	Enhancers	Aorta	Aorta

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