Variant report

Variant	rs1610072
Chromosome Location	chr5:114502968-114502969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:114497321..114503082-chr5:114503649..114507223,10	MCF-7	breast:
2	chr5:114499175..114500957-chr5:114501234..114503854,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152503	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10040143	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10059553	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11241316	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11738500	0.86[CEU][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs11745636	0.81[CHB][hapmap];0.81[TSI][hapmap]
rs12659682	0.81[CHB][hapmap]
rs12659716	0.81[CHB][hapmap]
rs1806346	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241974	0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs3805589	0.86[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3805590	0.91[CEU][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6594879	0.92[MKK][hapmap]
rs6594881	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6859943	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6894360	0.82[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes]
rs7719404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7737426	0.96[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap]
rs973	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs973589	0.80[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830453	chr5:114277261-114546536	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv462399	chr5:114445023-114526010	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv599477	chr5:114445023-114526010	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv830454	chr5:114453864-114607159	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1610072	CPNE7	trans	cerebellum	SCAN
rs1610072	TRIM36	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114472400-114504200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:114497600-114504200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:114499200-114503400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:114499800-114504000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
5	chr5:114500200-114503200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
6	chr5:114500200-114503200	ZNF genes & repeats	Brain Germinal Matrix	brain
7	chr5:114500400-114503200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
8	chr5:114500600-114503000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:114500600-114503000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:114500600-114503200	ZNF genes & repeats	Fetal Brain Female	brain
11	chr5:114500800-114503400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:114501200-114503600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
13	chr5:114501400-114503000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:114501400-114503000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
15	chr5:114501400-114503000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:114501400-114504800	Weak transcription	Gastric	stomach
17	chr5:114502000-114504200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:114502200-114503000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:114502600-114503000	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:114502800-114503600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr5:114502800-114504400	Weak transcription	Colonic Mucosa	Colon
22	chr5:114502800-114504800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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