Variant report

Variant	rs12303852
Chromosome Location	chr12:30905850-30905851
allele	A/G
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	POLR2A	chr12:30905583-30905908	HepG2	liver:	n/a	n/a
2	MYC	chr12:30905664-30905911	MCF10A-Er-Src	breast:	n/a	chr12:30905712-30905721
3	MAFK	chr12:30905233-30905868	K562	blood:	n/a	chr12:30905384-30905399 chr12:30905384-30905395 chr12:30905712-30905722 chr12:30905384-30905395 chr12:30905384-30905400
4	POLR2A	chr12:30905253-30909133	PBDE	blood:	n/a	n/a

Variant related genes	Relation type
CAPRIN2	TF binding region
ENSG00000246331	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10444423	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10743727	1.00[MEX][hapmap]
rs10743728	1.00[MEX][hapmap]
rs10743729	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10771748	1.00[MEX][hapmap]
rs10771752	1.00[MEX][hapmap]
rs10771755	1.00[MEX][hapmap]
rs10771765	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771766	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771767	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843804	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10843814	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10843816	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10843817	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10843822	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs10843824	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10843833	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051005	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs11051050	0.89[JPT][hapmap]
rs11051053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051061	0.90[JPT][hapmap]
rs12146709	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12305697	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370429	0.92[ASN][1000 genomes]
rs12370947	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12809335	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs12830910	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs14139	1.00[MEX][hapmap]
rs1866416	0.82[ASN][1000 genomes]
rs2241828	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2289300	1.00[MEX][hapmap]
rs2289302	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2304630	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs35925509	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3910561	1.00[MEX][hapmap]
rs3910564	1.00[MEX][hapmap]
rs4082413	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4143105	1.00[MEX][hapmap]
rs6487925	0.92[MEX][hapmap]
rs6487927	1.00[MEX][hapmap]
rs6487930	1.00[MEX][hapmap]
rs6487933	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs6487938	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297455	1.00[MEX][hapmap]
rs7304221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304976	0.92[ASN][1000 genomes]
rs7325	1.00[MEX][hapmap]
rs7327	1.00[MEX][hapmap]
rs7952744	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957226	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980510	0.85[CHB][hapmap];0.90[JPT][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12303852	IPO8	cis	Artery Tibial	GTEx
rs12303852	IPO8	cis	lymphoblastoid	seeQTL
rs12303852	IPO8	cis	multi-tissue	Pritchard

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30861400-30906200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:30861400-30906600	Weak transcription	Small Intestine	intestine
3	chr12:30863400-30906400	Weak transcription	Spleen	Spleen
4	chr12:30863400-30906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:30876000-30906600	Weak transcription	Fetal Intestine Small	intestine
6	chr12:30878200-30906200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:30878800-30906600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:30882000-30906800	Weak transcription	Psoas Muscle	Psoas
9	chr12:30882200-30906200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:30882200-30906400	Weak transcription	Lung	lung
11	chr12:30882200-30906400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:30882200-30906600	Weak transcription	Placenta	Placenta
13	chr12:30882200-30906800	Weak transcription	Esophagus	oesophagus
14	chr12:30882400-30906600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:30882600-30906200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:30882600-30906400	Weak transcription	Right Ventricle	heart
17	chr12:30882800-30906800	Weak transcription	Gastric	stomach
18	chr12:30883200-30906400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr12:30886600-30906400	Weak transcription	Brain Substantia Nigra	brain
20	chr12:30888400-30906800	Weak transcription	Fetal Intestine Large	intestine
21	chr12:30889200-30906200	Weak transcription	Thymus	Thymus
22	chr12:30892400-30906400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:30892400-30906400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:30892600-30906400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:30894800-30906400	Weak transcription	Stomach Mucosa	stomach
26	chr12:30897200-30906600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:30899600-30906600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr12:30900000-30906200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:30900000-30906200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr12:30900000-30906200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:30900000-30906400	Weak transcription	Adipose Nuclei	Adipose
32	chr12:30900000-30906400	Weak transcription	Fetal Muscle Leg	muscle
33	chr12:30900000-30906600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:30900000-30906600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr12:30900000-30906800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:30900200-30906200	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:30900200-30906400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:30900400-30906000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:30900400-30906200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr12:30900400-30906400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr12:30900400-30906400	Weak transcription	Fetal Brain Male	brain
42	chr12:30900400-30906400	Weak transcription	Left Ventricle	heart
43	chr12:30900400-30906400	Weak transcription	Ovary	ovary
44	chr12:30900600-30906600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:30901000-30906200	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr12:30901000-30906600	Weak transcription	Liver	Liver
47	chr12:30901200-30906000	Weak transcription	Fetal Lung	lung
48	chr12:30901200-30906400	Weak transcription	Fetal Brain Female	brain
49	chr12:30902200-30906800	Weak transcription	Aorta	Aorta
50	chr12:30903000-30906400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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