Variant report

Variant	rs12308822
Chromosome Location	chr12:30853447-30853448
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr12:30853149-30853722	SK-N-SH	brain:	n/a	chr12:30853376-30853385 chr12:30853378-30853389 chr12:30853375-30853387 chr12:30853377-30853384 chr12:30853377-30853385
2	EP300	chr12:30853431-30853707	SK-N-SH_RA	brain:	n/a	n/a
3	NFIC	chr12:30853072-30853599	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr12:30853078-30853686	SK-N-SH	brain:	n/a	n/a
5	FOS	chr12:30853290-30853526	MCF10A-Er-Src	breast:	n/a	chr12:30853376-30853385 chr12:30853378-30853389 chr12:30853375-30853387 chr12:30853377-30853384 chr12:30853377-30853385
6	GATA3	chr12:30853024-30853840	SK-N-SH	brain:	n/a	chr12:30853571-30853581
7	EP300	chr12:30853125-30853602	SK-N-SH_RA	brain:	n/a	chr12:30853376-30853385 chr12:30853377-30853386
8	MAFK	chr12:30853417-30853835	IMR90	lung:	n/a	chr12:30853641-30853656
9	FOSL2	chr12:30853121-30853700	SK-N-SH	brain:	n/a	chr12:30853376-30853385 chr12:30853378-30853389 chr12:30853375-30853387 chr12:30853377-30853384 chr12:30853377-30853385

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:30848462..30850744-chr12:30852619..30855375,2	K562	blood:
2	chr12:30853082..30854852-chr12:30907292..30909990,2	K562	blood:

Variant related genes	Relation type
IPO8	TF binding region
ENSG00000246331	Chromatin interaction
ENSG00000133704	Chromatin interaction
ENSG00000110888	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10743725	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10843794	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10843797	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10843798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10843803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10843805	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11051006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs11051009	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11051023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11051026	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11051030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11051034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11051044	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051046	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610452	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306961	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12310942	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12315407	0.87[AMR][1000 genomes]
rs12315446	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12371883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12372023	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2099028	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3888018	0.83[GIH][hapmap];1.00[MEX][hapmap]
rs3906774	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56705455	0.87[AMR][1000 genomes]
rs57153590	0.85[AMR][1000 genomes]
rs59483134	0.85[ASN][1000 genomes]
rs6487924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6487929	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6487931	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7135005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302606	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7302757	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303665	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306125	0.92[ASW][hapmap];0.94[CEU][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7307432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308638	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310127	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7315859	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73292874	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs74083892	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7955626	0.82[AMR][1000 genomes]
rs7963438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7963524	0.94[ASN][1000 genomes]
rs7968669	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7972061	0.82[AMR][1000 genomes]
rs7974251	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9651844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12308822	IPO8	cis	multi-tissue	Pritchard

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30849200-30881600	Weak transcription	Right Ventricle	heart
2	chr12:30849400-30853800	Weak transcription	HSMMtube	muscle
3	chr12:30849400-30854200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:30849400-30860600	Weak transcription	NH-A	brain
5	chr12:30849400-30861000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:30849400-30862800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:30849400-30866200	Weak transcription	Fetal Brain Male	brain
8	chr12:30849600-30853600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:30849600-30853600	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:30849600-30853600	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:30849600-30853600	Weak transcription	NHDF-Ad	bronchial
12	chr12:30849600-30853800	Weak transcription	Brain Angular Gyrus	brain
13	chr12:30849600-30861200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:30849600-30861800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:30849600-30861800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:30849600-30861800	Weak transcription	NHEK	skin
17	chr12:30849600-30862000	Weak transcription	Brain Germinal Matrix	brain
18	chr12:30849600-30862000	Weak transcription	HMEC	breast
19	chr12:30849600-30862200	Weak transcription	Brain Anterior Caudate	brain
20	chr12:30849600-30862200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:30849600-30862400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:30849600-30862600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:30849600-30881200	Weak transcription	Psoas Muscle	Psoas
24	chr12:30849600-30881600	Weak transcription	Aorta	Aorta
25	chr12:30849800-30853600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr12:30849800-30861800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr12:30849800-30861800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:30849800-30862000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:30849800-30862000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr12:30849800-30862000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:30849800-30862200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:30849800-30862400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:30849800-30862400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:30849800-30862400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:30849800-30862400	Weak transcription	Lung	lung
36	chr12:30849800-30862600	Weak transcription	Ovary	ovary
37	chr12:30849800-30862800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:30849800-30862800	Weak transcription	Brain Substantia Nigra	brain
39	chr12:30849800-30862800	Weak transcription	Left Ventricle	heart
40	chr12:30849800-30862800	Weak transcription	Pancreas	Pancrea
41	chr12:30849800-30867000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:30850000-30860800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:30850200-30861800	Weak transcription	Dnd41	blood
44	chr12:30852600-30854200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:30852600-30854400	Enhancers	Osteobl	bone
46	chr12:30853000-30854000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:30853000-30854400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:30853200-30853600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:30853400-30854200	Enhancers	Brain Cingulate Gyrus	brain
50	chr12:30853400-30854200	Enhancers	HSMM	muscle

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