Variant report

Variant	rs6487105
Chromosome Location	chr12:20678518-20678519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10770665	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10770668	0.85[CHB][hapmap]
rs10841556	0.84[JPT][hapmap]
rs10841557	0.81[JPT][hapmap]
rs10841558	0.87[ASN][1000 genomes]
rs10841560	0.86[ASN][1000 genomes]
rs10841561	0.84[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs11045285	0.81[JPT][hapmap]
rs11045294	0.84[ASN][1000 genomes]
rs12423118	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12425566	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12813387	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs12822341	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2311	0.82[CHB][hapmap]
rs4304839	0.85[CHB][hapmap]
rs4353322	0.84[CHB][hapmap]
rs4502032	0.82[CHB][hapmap]
rs4561252	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4762969	0.81[JPT][hapmap]
rs4762970	0.85[CHB][hapmap]
rs4762971	0.86[CHB][hapmap]
rs57544392	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6487101	0.86[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap]
rs6487103	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6487104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7131827	0.86[CHB][hapmap]
rs7303620	0.81[CHB][hapmap]
rs73075154	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7308219	0.86[ASN][1000 genomes]
rs7308418	0.86[CHB][hapmap]
rs7316700	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7487165	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7488735	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7488869	0.82[JPT][hapmap]
rs7955323	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7955819	0.96[ASN][1000 genomes]
rs7959560	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs7965577	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7969959	0.91[CHB][hapmap];0.81[JPT][hapmap]

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	nsv1048067	chr12:20363755-20874845	Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv541408	chr12:20363755-20874845	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1046870	chr12:20509914-20711535	Active TSS Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv541409	chr12:20509914-20711535	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
5	nsv1043890	chr12:20659151-21309993	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv541410	chr12:20659151-21309993	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6487105	ST8SIA1	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:20667600-20680200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:20670800-20679400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:20671000-20679800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr12:20673800-20680800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:20673800-20694200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:20673800-20704200	Weak transcription	Fetal Intestine Large	intestine
7	chr12:20674000-20679600	Weak transcription	Brain Anterior Caudate	brain
8	chr12:20674000-20680600	Weak transcription	Fetal Lung	lung
9	chr12:20674000-20681000	Weak transcription	Ovary	ovary
10	chr12:20674200-20679600	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:20675000-20680400	Weak transcription	Fetal Stomach	stomach
12	chr12:20675000-20680400	Weak transcription	Left Ventricle	heart
13	chr12:20675200-20680200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:20675200-20680200	Weak transcription	Fetal Intestine Small	intestine
15	chr12:20675600-20680400	Enhancers	Osteobl	bone
16	chr12:20676400-20679000	Enhancers	A549	lung
17	chr12:20676600-20679600	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:20677000-20680200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:20677200-20680600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:20677200-20681200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:20677400-20679000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:20677400-20680000	Weak transcription	NHDF-Ad	bronchial
23	chr12:20677400-20680200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:20677400-20680400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:20677400-20681000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:20677400-20681400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:20677600-20680200	Weak transcription	Hela-S3	cervix
28	chr12:20678000-20679000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:20678000-20681000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:20678200-20680200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:20678400-20679800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:20678400-20680400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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