Variant report

Variant	rs12823422
Chromosome Location	chr12:29423052-29423053
allele	C/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	REST	chr12:29422934-29423385	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
FAR2	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10492383	0.82[EUR][1000 genomes]
rs11608616	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11609540	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11610197	0.84[EUR][1000 genomes]
rs11610910	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11611420	0.82[EUR][1000 genomes]
rs11611687	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11612172	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11613628	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11614129	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11614901	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11615636	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12314737	0.86[ASN][1000 genomes]
rs12809077	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12809493	0.80[AMR][1000 genomes]
rs12810064	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12810315	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12811723	0.84[EUR][1000 genomes]
rs12813520	0.82[EUR][1000 genomes]
rs12813789	0.86[EUR][1000 genomes]
rs12813996	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12814180	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12814930	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12815222	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12816511	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817163	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817578	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12817825	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12817985	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12819896	0.84[EUR][1000 genomes]
rs12821498	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12821559	0.81[EUR][1000 genomes]
rs12821708	0.84[EUR][1000 genomes]
rs12822770	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12823372	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12823485	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12823903	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12824407	0.84[EUR][1000 genomes]
rs12826064	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12829666	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12830274	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12830493	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12830678	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12830906	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12831730	0.84[EUR][1000 genomes]
rs12832038	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12832263	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16934061	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1988943	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2350312	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882377	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34162895	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs35618989	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35636563	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36126531	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3764952	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4369447	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67280216	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67324531	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7134744	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7295387	0.84[EUR][1000 genomes]
rs7299158	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7299635	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7299663	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7308372	0.84[EUR][1000 genomes]
rs7314594	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7961336	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7964254	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7979654	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12823422	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12823422	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs12823422	RP11-996F15.2	cis	Artery Tibial	GTEx
rs12823422	RP11-996F15.2	cis	Muscle Skeletal	GTEx
rs12823422	RP11-996F15.2	cis	lung	GTEx
rs12823422	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs12823422	RP11-996F15.2	cis	Esophagus Muscularis	GTEx
rs12823422	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs12823422	RP11-996F15.2	cis	Thyroid	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29408200-29423200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:29408200-29425800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:29408400-29424000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr12:29410000-29425800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:29410000-29426200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:29414000-29423400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:29414400-29434000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:29417200-29465400	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr12:29417800-29424400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:29418600-29423400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:29419200-29430600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:29419600-29428000	Weak transcription	Fetal Brain Female	brain
13	chr12:29419800-29430400	Weak transcription	Brain Angular Gyrus	brain
14	chr12:29420400-29435000	Weak transcription	HUVEC	blood vessel
15	chr12:29420600-29431600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:29421000-29423400	Weak transcription	Primary T cells from cord blood	blood
17	chr12:29421000-29424400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:29421000-29425000	Weak transcription	Esophagus	oesophagus
19	chr12:29421000-29432000	Weak transcription	Adipose Nuclei	Adipose
20	chr12:29421200-29426600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:29421400-29423400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:29421400-29425800	Weak transcription	Lung	lung
23	chr12:29421600-29423400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr12:29421600-29426000	Weak transcription	Fetal Intestine Small	intestine
25	chr12:29421600-29426200	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:29421800-29423200	Weak transcription	Dnd41	blood
27	chr12:29421800-29425800	Weak transcription	Spleen	Spleen
28	chr12:29421800-29426200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr12:29422000-29455600	Weak transcription	Left Ventricle	heart
30	chr12:29422000-29465000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:29422200-29425800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:29422200-29430400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:29422200-29434800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr12:29422400-29434400	Weak transcription	Fetal Kidney	kidney
35	chr12:29422600-29426000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:29422800-29423600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:29422800-29423600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:29422800-29423800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:29422800-29427000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr12:29423000-29423600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:29423000-29424800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:29423000-29425000	Weak transcription	Placenta	Placenta
43	chr12:29423000-29426000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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