Variant report

Variant	rs7245762
Chromosome Location	chr19:36563749-36563750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36562817..36565517-chr19:36604605..36606772,2	MCF-7	breast:
2	chr19:36543772..36546988-chr19:36561665..36565427,3	MCF-7	breast:
3	chr19:36562998..36565193-chr19:36602097..36603847,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161277	Chromatin interaction
ENSG00000105258	Chromatin interaction
ENSG00000105254	Chromatin interaction
ENSG00000105261	Chromatin interaction
ENSG00000075702	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10414679	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10418015	0.81[EUR][1000 genomes]
rs10420353	0.82[CHB][hapmap]
rs10423651	1.00[ASN][1000 genomes]
rs10425692	1.00[ASN][1000 genomes]
rs10426582	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12462432	0.92[ASN][1000 genomes]
rs12462632	0.98[ASN][1000 genomes]
rs12462674	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12972660	0.84[AMR][1000 genomes]
rs12976812	0.86[CHB][hapmap]
rs12977802	0.89[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12979093	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12981654	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs1548506	0.87[YRI][hapmap]
rs2023865	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2051800	0.88[YRI][hapmap]
rs2072606	0.95[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs2075474	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2079151	0.84[ASN][1000 genomes]
rs2239510	0.95[JPT][hapmap]
rs34906485	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35125548	1.00[ASN][1000 genomes]
rs35875194	0.94[ASN][1000 genomes]
rs3826995	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4461192	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs4805154	1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4805155	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4806252	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4806253	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4806280	0.89[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56034793	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62109743	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs721542	1.00[ASN][1000 genomes]
rs7247057	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7250448	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7257383	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];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259592	0.95[ASN][1000 genomes]
rs7260609	0.92[ASN][1000 genomes]
rs757223	0.88[YRI][hapmap]
rs8100250	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8103569	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]

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	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7245762	TEX101	cis	parietal	SCAN
rs7245762	ZNF573	cis	cerebellum	SCAN
rs7245762	PSG2	cis	parietal	SCAN
rs7245762	ZNF229	cis	parietal	SCAN
rs7245762	POLR2I	cis	multi-tissue	Pritchard
rs7245762	PHLDB3	cis	parietal	SCAN
rs7245762	PSG9	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36546400-36577600	Weak transcription	Esophagus	oesophagus
2	chr19:36546400-36584000	Weak transcription	Right Atrium	heart
3	chr19:36546600-36572400	Weak transcription	Lung	lung
4	chr19:36546600-36602200	Weak transcription	Colonic Mucosa	Colon
5	chr19:36546600-36604800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr19:36546800-36572000	Weak transcription	Primary T cells from cord blood	blood
7	chr19:36546800-36572800	Weak transcription	Primary B cells from cord blood	blood
8	chr19:36546800-36572800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr19:36546800-36580200	Weak transcription	Fetal Kidney	kidney
10	chr19:36546800-36588000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:36546800-36592200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:36546800-36601400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr19:36547600-36584200	Weak transcription	Fetal Heart	heart
14	chr19:36548200-36596400	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr19:36548400-36571000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:36548800-36567800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:36549600-36566600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:36549600-36567200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:36552000-36572400	Weak transcription	Liver	Liver
20	chr19:36555000-36593000	Weak transcription	Fetal Lung	lung
21	chr19:36556000-36601600	Weak transcription	Pancreas	Pancrea
22	chr19:36558200-36572400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr19:36558800-36574000	Weak transcription	Gastric	stomach
24	chr19:36559000-36572400	Weak transcription	Placenta	Placenta
25	chr19:36559200-36564000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:36559200-36570400	Weak transcription	GM12878-XiMat	blood
27	chr19:36559200-36572600	Weak transcription	Fetal Brain Female	brain
28	chr19:36559200-36572800	Weak transcription	Brain Germinal Matrix	brain
29	chr19:36560400-36565800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr19:36560400-36580200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr19:36560600-36564000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:36560800-36565600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr19:36561000-36570600	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr19:36561000-36572200	Weak transcription	Fetal Intestine Large	intestine
35	chr19:36561200-36569400	Strong transcription	Fetal Stomach	stomach
36	chr19:36561200-36570800	Strong transcription	Thymus	Thymus
37	chr19:36561200-36571000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr19:36561200-36587800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:36561200-36597600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr19:36561200-36597600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr19:36561200-36597600	Strong transcription	Dnd41	blood
42	chr19:36561200-36598200	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr19:36561200-36598400	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr19:36561400-36564800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr19:36561400-36587800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:36561400-36596400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr19:36561400-36596600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr19:36561600-36564200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:36561600-36567800	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:36561600-36572000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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