Variant report

Variant	rs814243
Chromosome Location	chr12:32437631-32437632
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1151038	0.83[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1151039	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1151045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs155201	0.85[ASN][1000 genomes]
rs161979	0.85[ASN][1000 genomes]
rs161980	0.85[ASN][1000 genomes]
rs161981	0.90[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs185487	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2129590	0.88[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2594000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs261868	0.85[ASN][1000 genomes]
rs261869	0.92[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs261870	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs261874	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs261875	0.87[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs261876	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs261877	1.00[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2632344	0.90[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2632359	0.95[CEU][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap]
rs2632365	0.81[CHD][hapmap]
rs2650137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2728704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2728705	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2728800	0.85[ASN][1000 genomes]
rs326633	0.81[CHD][hapmap]
rs708225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751720	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs792473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs792474	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs792861	0.90[ASN][1000 genomes]
rs792863	0.83[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs792866	0.88[ASN][1000 genomes]
rs806784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs813784	0.83[CEU][hapmap]
rs901598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv558171	chr12:32287259-32559693	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv832366	chr12:32328559-32511360	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs814243	CYP27A1	trans	lymphoblastoid	seeQTL
rs814243	TNFSF12-TNFSF13	trans	lymphoblastoid	seeQTL
rs814243	ACTN1	trans	lymphoblastoid	seeQTL
rs814243	TNFSF13	trans	lymphoblastoid	seeQTL
rs814243	LRRC16A	trans	lymphoblastoid	seeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32424600-32438000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:32425000-32437800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:32426600-32443400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:32426800-32442800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:32426800-32443200	Weak transcription	NH-A	brain
6	chr12:32426800-32446800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:32427000-32437800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:32427000-32438000	Weak transcription	Fetal Brain Female	brain
9	chr12:32427000-32443400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:32427000-32458600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:32427000-32459400	Weak transcription	Aorta	Aorta
12	chr12:32427000-32463000	Weak transcription	NHLF	lung
13	chr12:32427200-32463000	Weak transcription	Fetal Intestine Small	intestine
14	chr12:32427400-32445200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:32427600-32454400	Weak transcription	Primary B cells from cord blood	blood
16	chr12:32427800-32438200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:32434400-32438000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:32434800-32443000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:32435200-32448200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:32436200-32440200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:32436400-32438600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr12:32436400-32439800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr12:32436400-32440600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:32437000-32438200	Enhancers	H9 Cell Line	embryonic stem cell
25	chr12:32437000-32439000	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr12:32437200-32438200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr12:32437200-32439800	Enhancers	H1 Cell Line	embryonic stem cell
28	chr12:32437200-32440000	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr12:32437400-32438000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:32437400-32438000	Enhancers	Osteobl	bone
31	chr12:32437400-32438200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr12:32437400-32438400	Weak transcription	Ovary	ovary
33	chr12:32437400-32439000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr12:32437400-32440000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr12:32437600-32437800	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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