Variant report

Variant	rs2272495
Chromosome Location	chr12:105583877-105583878
allele	C/T
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	chr12:105583437-105583884	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr12:105583641-105584682	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr12:105583784-105583881	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
APPL2	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1014502	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10431460	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10459203	0.82[CEU][hapmap];0.81[CHD][hapmap]
rs10459204	0.82[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap]
rs1057110	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077896	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10861334	0.80[CEU][hapmap]
rs10861339	0.81[CEU][hapmap]
rs10861359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861361	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10861363	0.84[CEU][hapmap]
rs1109433	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11112369	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11112370	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11112372	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11112375	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11112376	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112379	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11112388	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112409	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11112412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11112415	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11112416	1.00[CEU][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11112421	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11112423	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11112432	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11831854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11832489	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11834277	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1196845	0.82[GIH][hapmap]
rs12228093	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228948	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12230762	0.80[ASN][1000 genomes]
rs12812433	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12815031	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12819309	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12823614	0.82[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap]
rs12830078	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1317955	1.00[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs1373552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1444611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1470381	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2166143	0.87[CEU][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap]
rs2293643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2293644	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2464176	0.91[ASN][1000 genomes]
rs28549976	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34075890	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34983773	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35462155	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35672903	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3736628	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3794222	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3794223	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3794224	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3794227	0.94[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3817607	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829296	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4964125	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4964334	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4964335	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4964336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4964338	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4964339	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4964340	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4964342	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55908437	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56693261	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73179994	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7485364	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs755604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8015	0.92[CEU][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs881279	1.00[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9919746	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[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	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv870352	chr12:105557770-105589263	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
4	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2272495	C12orf75	cis	cerebellum	SCAN
rs2272495	TDG	cis	parietal	SCAN
rs2272495	APPL2	cis	cerebellum	SCAN
rs2272495	KIAA1033	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105522600-105586000	Weak transcription	Stomach Mucosa	stomach
2	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:105558200-105587200	Weak transcription	Psoas Muscle	Psoas
4	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:105561400-105598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:105568000-105589400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:105571400-105617800	Weak transcription	K562	blood
8	chr12:105576000-105593200	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr12:105576000-105595600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:105576400-105585600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:105576400-105606000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:105577000-105607200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:105577200-105584000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:105577200-105584000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:105577200-105587400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:105577200-105589400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:105577200-105592200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr12:105577400-105592800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:105577400-105593600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr12:105577400-105616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:105577600-105589200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr12:105577800-105585600	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr12:105577800-105585800	Strong transcription	Brain Anterior Caudate	brain
24	chr12:105577800-105586400	Strong transcription	Brain Substantia Nigra	brain
25	chr12:105577800-105586800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:105577800-105589600	Strong transcription	Primary B cells from peripheral blood	blood
27	chr12:105577800-105591200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:105577800-105591400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr12:105577800-105592200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:105577800-105592600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:105577800-105593400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:105577800-105594200	Strong transcription	Fetal Intestine Large	intestine
33	chr12:105577800-105594400	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:105577800-105595200	Strong transcription	Left Ventricle	heart
35	chr12:105577800-105598600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:105577800-105598800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr12:105577800-105599400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:105577800-105602600	Strong transcription	Fetal Thymus	thymus
39	chr12:105577800-105603600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:105577800-105605400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr12:105577800-105605600	Strong transcription	Primary B cells from cord blood	blood
42	chr12:105577800-105607400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr12:105578000-105584000	Strong transcription	NHDF-Ad	bronchial
44	chr12:105578000-105585800	Strong transcription	Brain Hippocampus Middle	brain
45	chr12:105578000-105586200	Strong transcription	HUVEC	blood vessel
46	chr12:105578000-105586400	Strong transcription	Adipose Nuclei	Adipose
47	chr12:105578000-105588600	Strong transcription	Liver	Liver
48	chr12:105578000-105589400	Strong transcription	Primary T cells from cord blood	blood
49	chr12:105578000-105589400	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr12:105578000-105590800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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