Variant report

Variant	rs1196852
Chromosome Location	chr12:105582245-105582246
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	chr12:105581936-105582442	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr12:105582207-105582256	MCF-7	breast:	n/a	n/a
3	POLR2A	chr12:105581860-105582665	K562	blood:	n/a	n/a

Variant related genes	Relation type
APPL2	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10083185	0.84[ASW][hapmap];0.81[YRI][hapmap]
rs10778367	1.00[CHB][hapmap]
rs10861347	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs10861371	1.00[CHB][hapmap]
rs10861400	1.00[CHB][hapmap]
rs10861407	1.00[CHB][hapmap]
rs10861409	1.00[CHB][hapmap]
rs11112410	0.89[YRI][hapmap]
rs11112434	1.00[CHB][hapmap]
rs11112475	1.00[CHB][hapmap]
rs1196748	1.00[CHB][hapmap]
rs1196749	1.00[CHB][hapmap]
rs1196753	1.00[CHB][hapmap]
rs1196754	1.00[CHB][hapmap]
rs1196755	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1196756	1.00[CHB][hapmap]
rs1196757	0.83[EUR][1000 genomes]
rs1196760	1.00[CHB][hapmap]
rs1196763	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1196777	1.00[CHB][hapmap]
rs1196793	1.00[CHB][hapmap]
rs1196800	1.00[CHB][hapmap]
rs1196801	1.00[CHB][hapmap]
rs1196806	1.00[CHB][hapmap]
rs1196813	1.00[CHB][hapmap]
rs1196817	1.00[CHB][hapmap]
rs1196818	1.00[CHB][hapmap]
rs1196819	1.00[CHB][hapmap]
rs1196839	1.00[CHB][hapmap]
rs1196842	1.00[CHB][hapmap]
rs1196848	1.00[CHB][hapmap]
rs1196861	1.00[CHB][hapmap]
rs1196862	1.00[CHB][hapmap]
rs1196864	1.00[CHB][hapmap]
rs1196881	1.00[CHB][hapmap]
rs1211276	1.00[CHB][hapmap]
rs12312965	0.82[YRI][hapmap]
rs12822081	1.00[CHB][hapmap]
rs1621553	1.00[CHB][hapmap]
rs1663564	1.00[CHB][hapmap]
rs2440715	1.00[CHB][hapmap]
rs2888846	1.00[CHB][hapmap]
rs4390426	1.00[CHB][hapmap]
rs4545651	1.00[CHB][hapmap]
rs7299166	0.94[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7299225	1.00[CHB][hapmap]
rs7302174	1.00[CHB][hapmap]
rs7959385	1.00[CHB][hapmap]
rs7971630	0.84[ASW][hapmap];0.82[YRI][hapmap]
rs7975787	0.82[YRI][hapmap]
rs7978034	0.82[YRI][hapmap]
rs935240	1.00[CHB][hapmap]
rs935241	1.00[CHB][hapmap]
rs935244	1.00[CHB][hapmap]
rs9645791	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1196852	TDG	cis	parietal	SCAN
rs1196852	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL
rs1196852	KIAA1033	Cis_1M	lymphoblastoid	RTeQTL
rs1196852	ALDH1L2	cis	cerebellum	SCAN
rs1196852	KIAA1033	cis	Muscle Skeletal	GTEx
rs1196852	APPL2	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	chr12:105525400-105583200	Weak transcription	Fetal Heart	heart
3	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:105556200-105583400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:105558200-105587200	Weak transcription	Psoas Muscle	Psoas
6	chr12:105558800-105615200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:105561400-105598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:105568000-105589400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:105571400-105617800	Weak transcription	K562	blood
10	chr12:105576000-105593200	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr12:105576000-105595600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:105576400-105585600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:105576400-105606000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:105577000-105583800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:105577000-105607200	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:105577200-105584000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:105577200-105584000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:105577200-105587400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:105577200-105589400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:105577200-105592200	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr12:105577400-105592800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:105577400-105593600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:105577400-105616200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:105577600-105589200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:105577800-105583800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:105577800-105583800	Strong transcription	Fetal Kidney	kidney
27	chr12:105577800-105585600	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr12:105577800-105585800	Strong transcription	Brain Anterior Caudate	brain
29	chr12:105577800-105586400	Strong transcription	Brain Substantia Nigra	brain
30	chr12:105577800-105586800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:105577800-105589600	Strong transcription	Primary B cells from peripheral blood	blood
32	chr12:105577800-105591200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:105577800-105591400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr12:105577800-105592200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:105577800-105592600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:105577800-105593400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:105577800-105594200	Strong transcription	Fetal Intestine Large	intestine
38	chr12:105577800-105594400	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:105577800-105595200	Strong transcription	Left Ventricle	heart
40	chr12:105577800-105598600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:105577800-105598800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr12:105577800-105599400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:105577800-105602600	Strong transcription	Fetal Thymus	thymus
44	chr12:105577800-105603600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:105577800-105605400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr12:105577800-105605600	Strong transcription	Primary B cells from cord blood	blood
47	chr12:105577800-105607400	Strong transcription	Duodenum Mucosa	Duodenum
48	chr12:105578000-105584000	Strong transcription	NHDF-Ad	bronchial
49	chr12:105578000-105585800	Strong transcription	Brain Hippocampus Middle	brain
50	chr12:105578000-105586200	Strong transcription	HUVEC	blood vessel

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