Variant report

Variant	rs1627431
Chromosome Location	chr12:75962912-75962913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75955678..75958303-chr12:75962611..75964917,2	MCF-7	breast:
2	chr12:75961478..75964130-chr12:75966131..75968035,2	K562	blood:
3	chr12:75961729..75963400-chr12:76429164..76431160,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10785197	0.94[ASN][1000 genomes]
rs10879928	0.90[GIH][hapmap]
rs11180559	0.90[ASN][1000 genomes]
rs11180576	0.99[ASN][1000 genomes]
rs11180577	0.97[ASN][1000 genomes]
rs11180591	0.94[ASN][1000 genomes]
rs1147994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148005	0.88[CEU][hapmap]
rs1148006	0.83[CEU][hapmap]
rs12299578	0.99[ASN][1000 genomes]
rs1275474	0.90[GIH][hapmap]
rs1351328	0.96[ASN][1000 genomes]
rs1383098	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1383101	0.88[ASN][1000 genomes]
rs1480001	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1480002	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1542570	0.92[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1552040	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1611928	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1630753	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1679380	0.95[ASN][1000 genomes]
rs1697753	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795374	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1795380	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795382	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2620687	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2652022	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847669	0.83[CEU][hapmap]
rs3912214	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4882638	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs56904707	0.90[ASN][1000 genomes]
rs57091991	0.97[ASN][1000 genomes]
rs7297463	0.98[ASN][1000 genomes]
rs73185062	0.99[ASN][1000 genomes]
rs7960251	0.99[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
rs1627431	GLIPR1L2	cis	cerebellum	SCAN
rs1627431	GLIPR1	cis	cerebellum	SCAN
rs1627431	GLIPR1L2	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75954600-75964800	Weak transcription	Brain Substantia Nigra	brain
2	chr12:75958800-75965000	Weak transcription	Fetal Brain Female	brain
3	chr12:75959600-75963200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:75960200-75966000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:75961200-75963000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr12:75961200-75963400	Enhancers	Fetal Lung	lung
7	chr12:75961400-75963000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:75961400-75963000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:75961400-75963400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr12:75961600-75963000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:75961600-75963000	Enhancers	Fetal Stomach	stomach
12	chr12:75961800-75963000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:75962200-75963000	Enhancers	HMEC	breast
14	chr12:75962400-75963000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:75962400-75963000	Enhancers	Fetal Heart	heart
16	chr12:75962600-75964000	Weak transcription	Brain Angular Gyrus	brain
17	chr12:75962800-75965400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:75962800-75966000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links