Variant report

Variant	rs1875308
Chromosome Location	chr4:152201204-152201205
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152200533..152202067-chr4:152244855..152247196,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109686	Chromatin interaction

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	0.84[AMR][1000 genomes];0.98[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	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643490	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13134038	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13134365	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280280	0.83[CHB][hapmap]
rs2280283	1.00[CEU][hapmap]
rs2407165	1.00[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[TSI][hapmap];1.00[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[TSI][hapmap];0.84[AMR][1000 genomes];1.00[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[TSI][hapmap];1.00[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[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407406	0.82[GIH][hapmap]
rs2897657	0.82[GIH][hapmap]
rs3736502	1.00[CEU][hapmap]
rs4504229	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529031	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696229	0.82[GIH][hapmap]
rs4696235	0.82[GIH][hapmap]
rs6535764	1.00[CEU][hapmap]
rs6535778	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6535784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835206	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845400	0.81[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[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654306	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7656771	1.00[CEU][hapmap]
rs7659146	0.82[GIH][hapmap]
rs7668154	0.82[GIH][hapmap]
rs7668541	0.84[AMR][1000 genomes];1.00[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:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152182600-152211000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:152182800-152206000	Weak transcription	NHEK	skin
3	chr4:152188600-152204000	Weak transcription	Gastric	stomach
4	chr4:152189400-152202400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:152189400-152205800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:152190800-152208600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:152191200-152204200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:152194200-152202400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:152194200-152213200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:152196000-152204000	Weak transcription	Fetal Stomach	stomach
11	chr4:152196000-152218400	Weak transcription	Psoas Muscle	Psoas
12	chr4:152197800-152242400	Weak transcription	Aorta	Aorta
13	chr4:152198000-152202600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr4:152198200-152201400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:152198200-152205800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:152198400-152201800	Strong transcription	Fetal Intestine Small	intestine
17	chr4:152198600-152202000	Weak transcription	Stomach Mucosa	stomach
18	chr4:152198600-152203400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:152198600-152204600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:152198600-152204800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:152198600-152205000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:152198600-152205000	Weak transcription	Fetal Intestine Large	intestine
23	chr4:152198600-152205800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr4:152198800-152203200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr4:152198800-152204400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:152198800-152221800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:152198800-152242800	Weak transcription	Fetal Lung	lung
28	chr4:152199600-152201600	Enhancers	Left Ventricle	heart
29	chr4:152199600-152201600	Enhancers	Right Atrium	heart
30	chr4:152200000-152201600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr4:152200000-152201600	Enhancers	Right Ventricle	heart
32	chr4:152200600-152204200	Weak transcription	HUVEC	blood vessel
33	chr4:152200800-152201600	Enhancers	Liver	Liver
34	chr4:152200800-152202000	Enhancers	Ovary	ovary
35	chr4:152201000-152201600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:152201000-152201800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr4:152201000-152203400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:152201000-152204400	Genic enhancers	HepG2	liver
39	chr4:152201200-152201600	Enhancers	Lung	lung

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