Variant report

Variant	rs899659
Chromosome Location	chr12:76028979-76028980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:76001058..76002737-chr12:76026565..76029545,2	K562	blood:
2	chr12:76028709..76030372-chr12:76096874..76098526,2	MCF-7	breast:
3	chr12:76028267..76031112-chr12:76369417..76371857,2	MCF-7	breast:
4	chr12:76028950..76031256-chr12:76042854..76044405,2	MCF-7	breast:
5	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: 40 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10748283	0.82[ASN][1000 genomes]
rs10748284	0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[ASN][1000 genomes]
rs10785199	0.84[ASN][1000 genomes]
rs10785200	0.84[ASN][1000 genomes]
rs10879937	0.82[ASN][1000 genomes]
rs10879938	0.89[CHB][hapmap];0.90[JPT][hapmap];0.89[MKK][hapmap]
rs10879943	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10879944	0.91[ASN][1000 genomes]
rs10879945	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10879946	0.91[ASN][1000 genomes]
rs10879947	0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10879948	0.93[ASN][1000 genomes]
rs11180601	0.82[ASN][1000 genomes]
rs11180605	0.96[ASN][1000 genomes]
rs11495681	0.82[ASN][1000 genomes]
rs12310185	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1466464	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1871548	0.88[ASN][1000 genomes]
rs34767748	0.95[ASN][1000 genomes]
rs34952545	0.95[ASN][1000 genomes]
rs4882601	0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4882602	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4882637	0.92[ASN][1000 genomes]
rs4882639	0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4882640	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7137366	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs733880	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs733881	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs7958075	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7958490	0.89[ASN][1000 genomes]
rs7958760	0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7972231	0.89[ASN][1000 genomes]
rs7973399	0.89[ASN][1000 genomes]
rs7980645	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs899658	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];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	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs899659	GLIPR1L2	cis	parietal	SCAN
rs899659	KRR1	cis	cerebellum	SCAN
rs899659	GLIPR1L2	cis	Thyroid	GTEx
rs899659	GLIPR1L2	cis	lung	GTEx
rs899659	GLIPR1	cis	parietal	SCAN
rs899659	GLIPR1L2	cis	cerebellum	SCAN
rs899659	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL
rs899659	GLIPR1L2	cis	Nerve Tibial	GTEx
rs899659	GLIPR1	cis	cerebellum	SCAN
rs899659	GLIPR1L2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76018200-76029600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:76018400-76029400	Weak transcription	NHEK	skin
3	chr12:76025400-76030800	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr12:76025600-76032400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:76025800-76030200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:76026200-76030200	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr12:76026600-76029000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:76026600-76035000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:76027000-76029600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:76027000-76029600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:76027400-76029800	Enhancers	H1 Cell Line	embryonic stem cell
12	chr12:76027400-76030000	Enhancers	Fetal Lung	lung
13	chr12:76027600-76030200	Enhancers	HUVEC	blood vessel
14	chr12:76027600-76031000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr12:76027800-76031000	Enhancers	HepG2	liver
16	chr12:76028000-76030600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr12:76028200-76029600	Enhancers	Dnd41	blood
18	chr12:76028200-76030000	Enhancers	K562	blood
19	chr12:76028200-76030200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr12:76028200-76030800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr12:76028200-76031000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr12:76028400-76029000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr12:76028400-76030200	Enhancers	HSMM	muscle
24	chr12:76028400-76030400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:76028400-76030600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr12:76028600-76030400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr12:76028600-76030400	Enhancers	NHDF-Ad	bronchial
28	chr12:76028600-76030400	Enhancers	NHLF	lung
29	chr12:76028600-76030400	Enhancers	Osteobl	bone
30	chr12:76028600-76031000	Enhancers	NH-A	brain
31	chr12:76028800-76029200	Enhancers	A549	lung
32	chr12:76028800-76030400	Enhancers	H9 Cell Line	embryonic stem cell
33	chr12:76028800-76030400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:76028800-76030600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:76028800-76030800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:76028800-76031000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:76028800-76031000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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