Variant report

Variant	rs12192270
Chromosome Location	chr6:143962114-143962115
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11155314	0.82[MEX][hapmap]
rs12193892	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12196077	0.87[ASN][1000 genomes]
rs12196139	0.87[ASN][1000 genomes]
rs12197559	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[ASN][1000 genomes]
rs12197980	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199447	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12209438	0.87[ASN][1000 genomes]
rs12524982	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs12525974	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs13191026	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs13195900	0.86[EUR][1000 genomes]
rs13199178	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13214196	0.88[TSI][hapmap]
rs1338535	0.85[EUR][1000 genomes]
rs1539333	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17291151	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1884172	0.88[TSI][hapmap]
rs2328506	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2328507	0.89[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34196129	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34775537	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35286147	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35296418	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4424099	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56392216	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62427376	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62427377	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67470559	0.87[EUR][1000 genomes]
rs6911970	0.85[EUR][1000 genomes]
rs6932482	0.88[TSI][hapmap]
rs7745970	0.85[EUR][1000 genomes]
rs7757372	0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs9496699	0.82[TSI][hapmap];0.85[EUR][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	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1032369	chr6:143925374-144007513	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv604805	chr6:143930404-144005949	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv517253	chr6:143953672-143975157	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv33992	chr6:143957777-143966636	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12192270	ITGA11	trans	cerebellum	SCAN
rs12192270	AIG1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143917000-143973600	Weak transcription	Fetal Intestine Small	intestine
2	chr6:143955800-143967200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:143956000-143963200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:143956000-143965000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:143956000-143967600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr6:143956000-143973800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:143959000-143965000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:143959000-143968800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:143959000-143978400	Weak transcription	Left Ventricle	heart
10	chr6:143959200-143964600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr6:143959200-143973800	Weak transcription	Right Atrium	heart
12	chr6:143961400-143963400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:143961600-143969800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:143962000-143965000	Weak transcription	Primary T cells from cord blood	blood

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