Variant report

Variant	rs12829666
Chromosome Location	chr12:29524159-29524160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:29523685..29526010-chr12:29528444..29531156,2	MCF-7	breast:
2	chr12:29520656..29526421-chr12:29532315..29535324,6	MCF-7	breast:
3	chr12:29507582..29513596-chr12:29520320..29524566,6	K562	blood:

Variant related genes	Relation type
ENSG00000087502	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10492377	0.81[CEU][hapmap]
rs10492383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608616	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11609540	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610197	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610910	1.00[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11611420	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611687	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11612172	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11613628	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11614129	1.00[CEU][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11614901	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11615636	0.84[EUR][1000 genomes]
rs12314737	0.93[TSI][hapmap]
rs12809077	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12809493	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12810064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12811201	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12811723	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813520	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813731	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813789	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12813996	0.91[CEU][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12814180	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12814930	0.91[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12815222	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12816511	0.91[CEU][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12817163	0.83[EUR][1000 genomes]
rs12817578	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12817825	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12817985	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12819896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821498	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12821559	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822770	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12823372	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12823422	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12823485	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12823903	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12824407	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12826064	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12830274	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12830493	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12830678	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12830906	0.84[EUR][1000 genomes]
rs12831730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12832038	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12832263	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16934061	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1988943	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2350312	0.84[EUR][1000 genomes]
rs2882377	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35618989	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35636563	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36126531	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3764952	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4369447	1.00[CEU][hapmap]
rs67280216	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67324531	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7134744	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7295387	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299158	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7299635	0.81[AMR][1000 genomes]
rs7299663	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7308372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314594	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7961336	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7964254	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7979654	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][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	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
3	esv1796867	chr12:29501941-29524159	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12829666	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs12829666	RP11-996F15.2	cis	Artery Tibial	GTEx
rs12829666	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs12829666	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12829666	RP11-996F15.2	cis	lung	GTEx
rs12829666	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs12829666	ERGIC2	cis	lymphoblastoid	seeQTL
rs12829666	RP11-996F15.2	cis	Thyroid	GTEx
rs12829666	RP11-996F15.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:121 , 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	chr12:29490400-29524600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:29493600-29532600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:29494400-29532400	Weak transcription	Brain Substantia Nigra	brain
18	chr12:29494600-29532800	Weak transcription	Colonic Mucosa	Colon
19	chr12:29496400-29532200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:29497400-29532400	Weak transcription	Fetal Heart	heart
21	chr12:29499000-29532400	Weak transcription	Fetal Brain Female	brain
22	chr12:29499200-29526600	Weak transcription	Stomach Mucosa	stomach
23	chr12:29500200-29533400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr12:29503400-29532200	Weak transcription	HSMMtube	muscle
25	chr12:29504200-29525800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:29505000-29532400	Weak transcription	Brain Angular Gyrus	brain
27	chr12:29505200-29524600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:29507600-29532200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:29509400-29529800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:29510200-29532600	Weak transcription	Fetal Stomach	stomach
31	chr12:29510400-29533400	Weak transcription	Lung	lung
32	chr12:29511600-29532200	Weak transcription	HMEC	breast
33	chr12:29513000-29525800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:29513600-29525000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr12:29513800-29524600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr12:29514600-29524600	Strong transcription	Dnd41	blood
37	chr12:29515400-29524600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:29515400-29524600	Strong transcription	Primary B cells from cord blood	blood
39	chr12:29515400-29524600	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr12:29515600-29524800	Strong transcription	Placenta	Placenta
41	chr12:29515600-29532200	Weak transcription	Fetal Intestine Small	intestine
42	chr12:29516000-29533200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:29516600-29525200	Strong transcription	Primary hematopoietic stem cells	blood
44	chr12:29517000-29524600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:29517200-29524800	Strong transcription	Liver	Liver
46	chr12:29517400-29524800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr12:29517800-29524600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:29517800-29524600	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr12:29517800-29524600	Strong transcription	NH-A	brain
50	chr12:29518000-29524400	Strong transcription	HUES64 Cell Line	embryonic stem cell

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