Variant report

Variant	rs3912214
Chromosome Location	chr12:75944025-75944026
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75942788..75945762-chr12:75947332..75949083,2	K562	blood:
2	chr12:75942170..75945016-chr12:75945671..75947951,2	MCF-7	breast:
3	chr12:75939240..75941323-chr12:75943102..75945716,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10785197	0.89[ASN][1000 genomes]
rs10879928	0.90[GIH][hapmap];0.82[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs11180553	0.84[CHD][hapmap]
rs11180559	0.93[ASN][1000 genomes]
rs11180576	0.95[ASN][1000 genomes]
rs11180577	0.93[ASN][1000 genomes]
rs11180591	0.89[ASN][1000 genomes]
rs1147994	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148005	0.83[CEU][hapmap]
rs12299578	0.95[ASN][1000 genomes]
rs1275474	0.90[GIH][hapmap]
rs1351328	0.92[ASN][1000 genomes]
rs1383098	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1383101	0.84[ASN][1000 genomes]
rs1480001	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1480002	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1542570	0.94[JPT][hapmap]
rs1552040	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1611928	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1627431	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1630753	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1679380	0.90[ASN][1000 genomes]
rs1679381	0.82[CEU][hapmap]
rs1697753	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795374	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1795379	0.85[AFR][1000 genomes]
rs1795380	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795382	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2620687	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2652022	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882638	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs56904707	0.93[ASN][1000 genomes]
rs57091991	0.93[ASN][1000 genomes]
rs7297463	0.94[ASN][1000 genomes]
rs73185062	0.95[ASN][1000 genomes]
rs7960251	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3912214	GLIPR1L2	cis	cerebellum	SCAN
rs3912214	GLIPR1	cis	cerebellum	SCAN
rs3912214	GLIPR1L2	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75938600-75947200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:75939800-75944200	Weak transcription	Brain Germinal Matrix	brain
3	chr12:75939800-75944200	Weak transcription	A549	lung
4	chr12:75940200-75944800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr12:75942800-75945800	Weak transcription	Fetal Brain Male	brain
6	chr12:75942800-75947400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:75942800-75947400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:75943000-75947200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:75943000-75947200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:75943200-75945200	Enhancers	Fetal Lung	lung
11	chr12:75943400-75945600	Enhancers	HSMMtube	muscle
12	chr12:75943600-75945200	Enhancers	Fetal Kidney	kidney
13	chr12:75943600-75945200	Enhancers	HUVEC	blood vessel
14	chr12:75943800-75944200	Flanking Active TSS	Fetal Heart	heart
15	chr12:75943800-75944400	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr12:75943800-75944600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:75943800-75944600	Enhancers	Brain Substantia Nigra	brain
18	chr12:75943800-75944600	Enhancers	Duodenum Mucosa	Duodenum
19	chr12:75943800-75944600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr12:75943800-75944600	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr12:75943800-75944800	Enhancers	Right Atrium	heart
22	chr12:75943800-75945000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:75943800-75945000	Enhancers	Adipose Nuclei	Adipose
24	chr12:75943800-75945000	Enhancers	Ovary	ovary
25	chr12:75943800-75945000	Enhancers	NHDF-Ad	bronchial
26	chr12:75943800-75945000	Enhancers	NHLF	lung
27	chr12:75943800-75945200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:75943800-75945200	Enhancers	Fetal Muscle Leg	muscle
29	chr12:75943800-75945400	Enhancers	HSMM	muscle
30	chr12:75944000-75944600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:75944000-75944600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:75944000-75944600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr12:75944000-75944600	Enhancers	NH-A	brain
34	chr12:75944000-75945000	Enhancers	Stomach Mucosa	stomach

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