Variant report

Variant	rs12813520
Chromosome Location	chr12:29525530-29525531
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29523685..29526010-chr12:29528444..29531156,2	MCF-7	breast:
2	chr12:29520656..29526421-chr12:29532315..29535324,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000087502	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10492383	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608616	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11609540	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611420	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611687	0.82[EUR][1000 genomes]
rs11612172	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11613628	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11615636	0.82[EUR][1000 genomes]
rs12809493	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12810064	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810315	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12811201	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12811723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813731	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813789	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12813996	0.82[EUR][1000 genomes]
rs12814180	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12814930	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12815222	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12816511	0.81[EUR][1000 genomes]
rs12817163	0.81[EUR][1000 genomes]
rs12817578	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12817825	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12817985	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12819896	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821498	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12821559	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823372	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12823422	0.82[EUR][1000 genomes]
rs12823485	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12823903	0.82[EUR][1000 genomes]
rs12824407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12829666	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830274	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12830493	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12830678	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12830906	0.82[EUR][1000 genomes]
rs12831730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12832038	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12832263	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1988943	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2350312	0.82[EUR][1000 genomes]
rs2882377	0.82[EUR][1000 genomes]
rs35618989	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35636563	0.82[EUR][1000 genomes]
rs36126531	0.90[ASN][1000 genomes]
rs3764952	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67280216	0.82[EUR][1000 genomes]
rs7134744	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7295387	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308372	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314594	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7961336	0.82[EUR][1000 genomes]
rs7964254	0.82[EUR][1000 genomes]
rs7979654	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	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
2	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12813520	RP11-996F15.2	cis	Thyroid	GTEx
rs12813520	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12813520	RP11-996F15.2	cis	Artery Tibial	GTEx
rs12813520	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs12813520	RP11-996F15.2	cis	lung	GTEx
rs12813520	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs12813520	RP11-996F15.2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
2	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
3	chr12:29470800-29532800	Weak transcription	Right Ventricle	heart
4	chr12:29476200-29533400	Weak transcription	Pancreas	Pancrea
5	chr12:29476400-29532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:29476400-29533200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:29484200-29532000	Weak transcription	Fetal Brain Male	brain
8	chr12:29485600-29533400	Weak transcription	Gastric	stomach
9	chr12:29486800-29528600	Weak transcription	Psoas Muscle	Psoas
10	chr12:29487000-29533000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:29488800-29532000	Weak transcription	NHLF	lung
12	chr12:29489600-29525600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:29490000-29533400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:29490000-29533400	Weak transcription	Esophagus	oesophagus
15	chr12:29493600-29532600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:29494400-29532400	Weak transcription	Brain Substantia Nigra	brain
17	chr12:29494600-29532800	Weak transcription	Colonic Mucosa	Colon
18	chr12:29496400-29532200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:29497400-29532400	Weak transcription	Fetal Heart	heart
20	chr12:29499000-29532400	Weak transcription	Fetal Brain Female	brain
21	chr12:29499200-29526600	Weak transcription	Stomach Mucosa	stomach
22	chr12:29500200-29533400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:29503400-29532200	Weak transcription	HSMMtube	muscle
24	chr12:29504200-29525800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr12:29505000-29532400	Weak transcription	Brain Angular Gyrus	brain
26	chr12:29507600-29532200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:29509400-29529800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:29510200-29532600	Weak transcription	Fetal Stomach	stomach
29	chr12:29510400-29533400	Weak transcription	Lung	lung
30	chr12:29511600-29532200	Weak transcription	HMEC	breast
31	chr12:29513000-29525800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr12:29515600-29532200	Weak transcription	Fetal Intestine Small	intestine
33	chr12:29516000-29533200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:29518400-29527000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:29518400-29527400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:29518400-29529400	Weak transcription	Thymus	Thymus
37	chr12:29518400-29532200	Weak transcription	Brain Anterior Caudate	brain
38	chr12:29518400-29533200	Weak transcription	Ovary	ovary
39	chr12:29518600-29526200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr12:29518600-29532600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr12:29518800-29533000	Weak transcription	Fetal Muscle Leg	muscle
42	chr12:29519200-29532000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:29519200-29532800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:29519200-29533000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr12:29519400-29531600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr12:29519400-29531800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:29519400-29532000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr12:29519400-29532200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:29519400-29532400	Weak transcription	Brain Hippocampus Middle	brain
50	chr12:29520000-29529400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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