Variant report

Variant	rs7079728
Chromosome Location	chr10:97024814-97024815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:97023957..97026874-chr10:97030558..97032855,2	MCF-7	breast:
2	chr10:97022981..97025591-chr10:97038019..97040228,2	MCF-7	breast:
3	chr10:97023146..97026051-chr10:97049239..97052357,4	MCF-7	breast:
4	chr10:97023872..97028051-chr10:97048144..97051430,5	K562	blood:
5	chr10:97011474..97014381-chr10:97024033..97026286,2	K562	blood:
6	chr10:97019193..97020732-chr10:97024741..97026574,2	K562	blood:

Variant related genes	Relation type
ENSG00000107438	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10786194	0.88[ASW][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes]
rs11188253	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188254	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11596920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11597364	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12768190	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026679	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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296962	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296963	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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296964	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34566882	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737015	0.88[ASW][hapmap];0.98[LWK][hapmap];0.88[MKK][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes]
rs4917682	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4918907	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6583987	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7067902	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7068656	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7087560	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7095761	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7895650	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7910388	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7923547	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7079728	PCGF5	cis	cerebellum	SCAN
rs7079728	TMEM20	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96998400-97030200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:97007000-97026400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr10:97009200-97028200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr10:97016400-97026200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr10:97016800-97036000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr10:97018800-97030000	Weak transcription	Thymus	Thymus
7	chr10:97019400-97026400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr10:97020000-97026600	Genic enhancers	Fetal Intestine Large	intestine
9	chr10:97020200-97025000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr10:97020200-97026600	Genic enhancers	Fetal Intestine Small	intestine
11	chr10:97020200-97026600	Enhancers	Right Atrium	heart
12	chr10:97020400-97027000	Genic enhancers	HepG2	liver
13	chr10:97021000-97026200	Weak transcription	Colon Smooth Muscle	Colon
14	chr10:97021000-97026600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr10:97021000-97034400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr10:97021200-97025200	Strong transcription	GM12878-XiMat	blood
17	chr10:97021200-97025400	Weak transcription	Fetal Lung	lung
18	chr10:97021200-97026000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr10:97021200-97026200	Weak transcription	HUVEC	blood vessel
20	chr10:97021200-97026600	Genic enhancers	NHEK	skin
21	chr10:97021400-97025800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr10:97021400-97026000	Weak transcription	NH-A	brain
23	chr10:97021400-97026200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:97021400-97026200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr10:97021400-97036400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr10:97021600-97027800	Weak transcription	HSMM	muscle
27	chr10:97021800-97025600	Strong transcription	Liver	Liver
28	chr10:97022000-97027400	Genic enhancers	Primary B cells from peripheral blood	blood
29	chr10:97023000-97026400	Genic enhancers	Placenta	Placenta
30	chr10:97023000-97026800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
31	chr10:97023200-97025000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr10:97023200-97025000	Strong transcription	NHDF-Ad	bronchial
33	chr10:97023200-97028200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr10:97023200-97029200	Genic enhancers	HMEC	breast
35	chr10:97023200-97033000	Weak transcription	Psoas Muscle	Psoas
36	chr10:97023400-97025200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr10:97023400-97025600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr10:97023400-97028200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr10:97023600-97025400	Enhancers	Primary B cells from cord blood	blood
40	chr10:97023600-97026400	Weak transcription	Fetal Heart	heart
41	chr10:97023800-97028800	Weak transcription	Fetal Muscle Leg	muscle
42	chr10:97024000-97025000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr10:97024000-97025400	Strong transcription	Left Ventricle	heart
44	chr10:97024000-97026000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr10:97024000-97026400	Enhancers	H9 Cell Line	embryonic stem cell
46	chr10:97024000-97026400	Enhancers	Esophagus	oesophagus
47	chr10:97024200-97025000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr10:97024200-97025000	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr10:97024200-97025000	Enhancers	A549	lung
50	chr10:97024200-97025400	Weak transcription	Lung	lung

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