Variant report

Variant	rs7980645
Chromosome Location	chr12:76024710-76024711
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	chr12:76023357..76025100-chr12:76099295..76101249,2	MCF-7	breast:
2	chr12:76014354..76029119-chr12:76417641..76428409,36	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257453	Chromatin interaction
ENSG00000257839	Chromatin interaction
ENSG00000139289	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10748283	0.86[ASN][1000 genomes]
rs10748284	0.94[CHB][hapmap];0.94[ASN][1000 genomes]
rs10785199	0.84[ASN][1000 genomes]
rs10785200	0.84[ASN][1000 genomes]
rs10879937	0.86[ASN][1000 genomes]
rs10879938	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10879943	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10879944	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10879945	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10879946	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10879947	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879948	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11180600	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11180601	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11180605	0.93[ASN][1000 genomes]
rs11495681	0.85[ASN][1000 genomes]
rs12310185	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12318049	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1466464	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1480005	0.81[ASN][1000 genomes]
rs1871548	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34767748	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34952545	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4882601	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4882602	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4882637	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4882639	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882640	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7137366	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs733880	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs733881	0.95[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap]
rs7958075	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7958490	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7958760	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7972231	0.91[ASN][1000 genomes]
rs7973399	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs899658	0.96[ASN][1000 genomes]
rs899659	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[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	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7980645	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx
rs7980645	GLIPR1L2	cis	Artery Tibial	GTEx
rs7980645	KRR1	cis	parietal	SCAN
rs7980645	RP11-585P4.5	cis	Thyroid	GTEx
rs7980645	GLIPR1L2	cis	Thyroid	GTEx
rs7980645	GLIPR1L2	cis	cerebellum	SCAN
rs7980645	GLIPR1L2	cis	parietal	SCAN
rs7980645	KRR1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76017600-76025200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr12:76017800-76028800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:76018000-76025400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:76018000-76025400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:76018000-76028600	Weak transcription	NHLF	lung
6	chr12:76018000-76028800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:76018200-76029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:76018400-76025000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr12:76018400-76025200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:76018400-76027600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:76018400-76029400	Weak transcription	NHEK	skin
12	chr12:76023000-76026200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:76023400-76025400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:76023400-76025600	Weak transcription	Fetal Stomach	stomach
15	chr12:76023400-76028200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr12:76024000-76027800	Weak transcription	HepG2	liver
17	chr12:76024200-76025400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:76024200-76028400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:76024400-76025200	Weak transcription	Fetal Lung	lung
20	chr12:76024600-76026200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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