Variant report

Variant	rs10520102
Chromosome Location	chr4:152147441-152147442
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	PBX3	chr4:152147311-152147918	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr4:152147348-152147809	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr4:152147301-152147895	HUVEC	blood vessel:	n/a	n/a
4	JUND	chr4:152147293-152147935	HCT-116	colon:	n/a	n/a
5	FOSL2	chr4:152147234-152147936	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr4:152147181-152147897	SK-N-SH	brain:	n/a	chr4:152147663-152147670
7	EP300	chr4:152147335-152147992	SK-N-SH	brain:	n/a	n/a
8	FOSL1	chr4:152147358-152147928	HCT-116	colon:	n/a	n/a
9	JUND	chr4:152147211-152147962	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr4:152147023-152148020	SK-N-SH	brain:	n/a	n/a
11	STAT3	chr4:152147221-152147853	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr4:152147209-152150071	MCF10A-Er-Src	breast:	n/a	n/a
13	NFIC	chr4:152147117-152148051	SK-N-SH	brain:	n/a	n/a
14	FOSL2	chr4:152147363-152147755	SK-N-SH	brain:	n/a	n/a
15	MAZ	chr4:152147325-152148138	IMR90	lung:	n/a	n/a
16	STAT3	chr4:152147429-152147723	MCF10A-Er-Src	breast:	n/a	n/a
17	GATA3	chr4:152147256-152147904	SK-N-SH	brain:	n/a	chr4:152147663-152147670
18	FOS	chr4:152147397-152147785	MCF10A-Er-Src	breast:	n/a	n/a
19	MAFK	chr4:152147395-152147878	IMR90	lung:	n/a	n/a
20	PBX3	chr4:152147199-152147897	SK-N-SH	brain:	n/a	n/a
21	FOS	chr4:152147381-152147889	MCF10A-Er-Src	breast:	n/a	n/a
22	JUND	chr4:152147270-152147955	SK-N-SH	brain:	n/a	n/a
23	E2F4	chr4:152147292-152147959	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr4:152147319-152147876	IMR90	lung:	n/a	n/a
25	NFIC	chr4:152147358-152147881	SK-N-SH	brain:	n/a	n/a
26	TCF12	chr4:152146957-152147978	SK-N-SH	brain:	n/a	n/a
27	FOS	chr4:152147353-152148414	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr4:152147344-152147878	MCF10A-Er-Src	breast:	n/a	n/a
29	STAT3	chr4:152147270-152147737	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr4:152147294-152147755	U87	brain:	n/a	n/a
31	JUND	chr4:152147321-152147856	HCT-116	colon:	n/a	n/a
32	POLR2A	chr4:152147184-152147853	U87	brain:	n/a	n/a
33	SP1	chr4:152147331-152147937	HCT-116	colon:	n/a	chr4:152147638-152147651
34	JUND	chr4:152147262-152148177	SK-N-SH	brain:	n/a	n/a
35	FOSL1	chr4:152147202-152147964	HCT-116	colon:	n/a	n/a
36	MYC	chr4:152147434-152147736	MCF10A-Er-Src	breast:	n/a	n/a
37	SP1	chr4:152147272-152147816	HCT-116	colon:	n/a	chr4:152147638-152147651
38	JUN	chr4:152147373-152147803	HUVEC	blood vessel:	n/a	n/a
39	FOSL2	chr4:152147321-152147854	A549	lung:	n/a	n/a
40	FOS	chr4:152147303-152147870	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr4:152147357-152147771	HUVEC	blood vessel:	n/a	n/a
42	FOS	chr4:152147265-152148444	MCF10A-Er-Src	breast:	n/a	n/a
43	MYC	chr4:152147294-152147840	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SH3D19	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10016092	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10020297	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10020317	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs10434137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461255	0.87[EUR][1000 genomes]
rs10520101	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10776522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10857253	0.89[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs11099792	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11099793	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11099796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11733964	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs11734577	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs11934792	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs11945206	0.99[ASN][1000 genomes]
rs12505974	0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs12508270	0.85[JPT][hapmap]
rs12644496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12647306	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13101417	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs13103344	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13111753	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13122609	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13125574	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13141515	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs13145829	0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs17633530	0.85[JPT][hapmap]
rs17633600	0.85[JPT][hapmap]
rs2280280	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2280283	0.85[JPT][hapmap]
rs2407222	0.99[ASN][1000 genomes]
rs2407223	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2407407	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2407408	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2407409	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2407410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2407412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2407413	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2407417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2407418	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407431	0.83[EUR][1000 genomes]
rs2897655	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2897656	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2897659	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs3736502	0.85[JPT][hapmap]
rs3792611	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4266274	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4312738	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4467540	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4591577	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696239	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696658	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs6535764	0.85[JPT][hapmap]
rs6846323	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs6847934	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7439970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7656771	0.85[JPT][hapmap]
rs7664483	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs7669180	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs7688786	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691584	0.95[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	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
6	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv870229	chr4:152114410-152161072	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152117600-152148800	Weak transcription	Esophagus	oesophagus
2	chr4:152120800-152153800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:152129000-152148800	Weak transcription	Fetal Intestine Large	intestine
4	chr4:152129000-152168000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:152129200-152148800	Weak transcription	Liver	Liver
6	chr4:152129400-152167800	Weak transcription	Right Ventricle	heart
7	chr4:152130200-152187800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr4:152136600-152158000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:152137400-152148800	Weak transcription	Left Ventricle	heart
10	chr4:152139400-152147600	Weak transcription	Fetal Heart	heart
11	chr4:152141000-152167400	Weak transcription	HepG2	liver
12	chr4:152144400-152147800	Weak transcription	Fetal Intestine Small	intestine
13	chr4:152144800-152149200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr4:152144800-152163400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr4:152145800-152147800	Active TSS	NHLF	lung
16	chr4:152145800-152148800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:152145800-152148800	Active TSS	NHDF-Ad	bronchial
18	chr4:152145800-152149600	Active TSS	Right Atrium	heart
19	chr4:152146000-152148800	Active TSS	Adipose Nuclei	Adipose
20	chr4:152146000-152149000	Active TSS	Ovary	ovary
21	chr4:152146000-152149200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:152146000-152149200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:152146000-152149400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:152146200-152149800	Flanking Active TSS	HUVEC	blood vessel
25	chr4:152146400-152147800	Active TSS	Muscle Satellite Cultured Cells	--
26	chr4:152146600-152147600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr4:152146600-152147800	Active TSS	NH-A	brain
28	chr4:152146600-152148600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:152146600-152149600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:152146800-152147600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:152146800-152147600	Active TSS	Fetal Stomach	stomach
32	chr4:152146800-152147600	Active TSS	HSMMtube	muscle
33	chr4:152146800-152147600	Active TSS	Osteobl	bone
34	chr4:152146800-152147800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:152146800-152147800	Active TSS	HSMM	muscle
36	chr4:152146800-152149000	Active TSS	Fetal Muscle Leg	muscle
37	chr4:152146800-152149200	Active TSS	Brain Angular Gyrus	brain
38	chr4:152147000-152148200	Flanking Active TSS	HMEC	breast
39	chr4:152147000-152148800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:152147000-152149000	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
41	chr4:152147000-152149000	Active TSS	Placenta Amnion	Placenta Amnion
42	chr4:152147000-152149200	Active TSS	Brain Cingulate Gyrus	brain
43	chr4:152147000-152149200	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr4:152147000-152149400	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr4:152147200-152147600	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr4:152147200-152147800	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr4:152147200-152148000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:152147200-152148000	Active TSS	Fetal Muscle Trunk	muscle
49	chr4:152147200-152148000	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr4:152147200-152148000	Flanking Active TSS	NHEK	skin

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