Variant report

Variant	rs4504229
Chromosome Location	chr4:152187952-152187953
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	FOXA1	chr4:152187693-152188766	HepG2	liver:	n/a	n/a
2	FOXA1	chr4:152187715-152188190	HepG2	liver:	n/a	n/a
3	FOS	chr4:152187801-152188034	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr4:152187829-152188026	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr4:152187769-152188240	HUVEC	blood vessel:	n/a	n/a
6	FOXA2	chr4:152187856-152188198	HepG2	liver:	n/a	n/a
7	BHLHE40	chr4:152187926-152188543	HepG2	liver:	n/a	n/a
8	FOS	chr4:152187881-152188003	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SH3D19	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10006188	0.96[ASN][1000 genomes]
rs10020317	0.81[GIH][hapmap]
rs10030785	0.85[GIH][hapmap]
rs10032413	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10857254	0.82[GIH][hapmap]
rs11734577	0.81[GIH][hapmap]
rs11734586	0.82[GIH][hapmap]
rs11938266	0.82[GIH][hapmap]
rs12505974	0.81[GIH][hapmap]
rs12509608	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643490	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134038	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13134365	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280280	0.83[CHB][hapmap]
rs2280283	1.00[CEU][hapmap]
rs2407165	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407406	0.82[GIH][hapmap]
rs2897657	0.82[GIH][hapmap]
rs3736502	1.00[CEU][hapmap]
rs4529031	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696229	0.82[GIH][hapmap]
rs4696235	0.82[GIH][hapmap]
rs6535764	1.00[CEU][hapmap]
rs6535778	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6535784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835206	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845400	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6846323	0.81[GIH][hapmap]
rs6847927	0.82[GIH][hapmap]
rs6850311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654306	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7656771	1.00[CEU][hapmap]
rs7659146	0.82[GIH][hapmap]
rs7668154	0.82[GIH][hapmap]
rs7668541	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669180	0.81[GIH][hapmap]
rs7690329	0.82[GIH][hapmap]

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	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	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
5	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

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152149200-152197600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:152165400-152189000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:152172800-152190600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:152173400-152189400	Weak transcription	Aorta	Aorta
5	chr4:152173800-152198200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:152174000-152192200	Weak transcription	Brain Angular Gyrus	brain
7	chr4:152177400-152198200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:152177800-152200000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:152178200-152188200	Weak transcription	Liver	Liver
10	chr4:152180000-152193800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:152180200-152189000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:152180800-152191000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:152182600-152189000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:152182600-152211000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:152182800-152206000	Weak transcription	NHEK	skin
16	chr4:152183200-152198200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:152184200-152188400	Weak transcription	Psoas Muscle	Psoas
18	chr4:152184400-152192400	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:152184600-152188000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:152185000-152188200	Weak transcription	Ovary	ovary
21	chr4:152185000-152191200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:152185000-152198200	Weak transcription	Right Ventricle	heart
23	chr4:152185200-152197600	Weak transcription	Left Ventricle	heart
24	chr4:152187000-152189400	Enhancers	HepG2	liver
25	chr4:152187400-152189400	Enhancers	Fetal Intestine Small	intestine
26	chr4:152187600-152188200	Enhancers	Muscle Satellite Cultured Cells	--
27	chr4:152187600-152189000	Enhancers	HUVEC	blood vessel
28	chr4:152187600-152189400	Enhancers	Fetal Intestine Large	intestine
29	chr4:152187800-152189000	Enhancers	Duodenum Mucosa	Duodenum

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