Variant report

Variant	rs10879943
Chromosome Location	chr12:76017928-76017929
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:76017394..76018226-chr12:76424820..76425629,3	MCF-7	breast:
2	chr12:76015495..76018360-chr12:76104509..76107219,2	MCF-7	breast:
3	chr12:76013741..76020372-chr12:76422912..76427305,12	MCF-7	breast:
4	chr12:76017749..76018271-chr12:76430624..76431420,2	MCF-7	breast:
5	chr12:76017307..76018172-chr12:76430579..76431583,4	MCF-7	breast:
6	chr12:76017499..76019528-chr12:76384312..76386033,2	MCF-7	breast:
7	chr12:76015734..76021626-chr12:76097256..76101818,9	MCF-7	breast:
8	chr12:76017332..76018157-chr12:76849234..76849752,2	MCF-7	breast:
9	chr12:76014354..76029119-chr12:76417641..76428409,36	MCF-7	breast:
10	chr12:76017322..76018337-chr12:76425217..76425917,6	MCF-7	breast:
11	chr12:76017185..76019394-chr12:76337259..76339909,2	MCF-7	breast:
12	chr12:76017340..76020194-chr12:76022357..76024091,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLIPR1-6	chr12:76017303-76017952	NONHSAT029538

No data

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

Extended variants
information (count: 44 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10748283	0.89[ASN][1000 genomes]
rs10748284	0.84[CHB][hapmap];0.84[JPT][hapmap];0.84[YRI][hapmap];0.82[ASN][1000 genomes]
rs10785199	0.87[ASN][1000 genomes]
rs10785200	0.87[ASN][1000 genomes]
rs10879937	0.89[ASN][1000 genomes]
rs10879938	0.86[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs10879944	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10879945	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10879946	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10879947	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.80[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10879948	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11180600	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11180601	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11180605	0.83[ASN][1000 genomes]
rs11495681	0.88[ASN][1000 genomes]
rs12310185	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12318049	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1466464	0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1480005	0.84[ASN][1000 genomes]
rs1871548	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34767748	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34952545	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4882601	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4882602	0.96[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4882637	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4882639	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4882640	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7137366	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs733880	0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs733881	0.90[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7956799	0.80[ASN][1000 genomes]
rs7958075	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7958490	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7958760	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7972231	0.89[ASN][1000 genomes]
rs7973399	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7980645	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]
rs899658	0.84[ASN][1000 genomes]
rs899659	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10879943	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs10879943	RP11-585P4.5	cis	Thyroid	GTEx
rs10879943	GLIPR1L2	cis	cerebellum	SCAN
rs10879943	KRR1	cis	parietal	SCAN
rs10879943	GLIPR1L2	cis	Thyroid	GTEx
rs10879943	GLIPR1L2	cis	parietal	SCAN
rs10879943	GLIPR1L2	cis	Artery Tibial	GTEx
rs10879943	KRR1	cis	cerebellum	SCAN
rs10879943	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76015600-76018600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:76016200-76018200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr12:76016200-76018200	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr12:76016200-76018400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr12:76016400-76018000	Enhancers	HUVEC	blood vessel
6	chr12:76016400-76018400	Enhancers	NHEK	skin
7	chr12:76016400-76018600	Enhancers	Hela-S3	cervix
8	chr12:76016400-76018600	Enhancers	HepG2	liver
9	chr12:76016600-76018000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:76016800-76018000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:76016800-76018000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:76016800-76020800	Weak transcription	K562	blood
13	chr12:76017000-76018000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:76017000-76018000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:76017000-76018000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr12:76017000-76018000	Enhancers	Fetal Heart	heart
17	chr12:76017000-76018200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:76017200-76018000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:76017200-76018200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:76017200-76018200	Enhancers	NHDF-Ad	bronchial
21	chr12:76017400-76018000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:76017400-76018000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr12:76017400-76018000	Enhancers	Adipose Nuclei	Adipose
24	chr12:76017400-76018000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr12:76017400-76018000	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr12:76017400-76018000	Enhancers	HSMMtube	muscle
27	chr12:76017400-76018000	Enhancers	NHLF	lung
28	chr12:76017400-76018200	Enhancers	HMEC	breast
29	chr12:76017400-76018400	Enhancers	A549	lung
30	chr12:76017400-76018800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:76017600-76018000	Enhancers	H9 Cell Line	embryonic stem cell
32	chr12:76017600-76018000	Enhancers	Liver	Liver
33	chr12:76017600-76018400	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr12:76017600-76018400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr12:76017600-76018400	Enhancers	Fetal Intestine Small	intestine
36	chr12:76017600-76025200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:76017800-76018200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:76017800-76018400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:76017800-76018400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:76017800-76021400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr12:76017800-76021400	Weak transcription	Pancreas	Pancrea
42	chr12:76017800-76022600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:76017800-76028800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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