Variant report

Variant	rs12612729
Chromosome Location	chr2:113957048-113957049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113931492..113932996-chr2:113955583..113957836,2	MCF-7	breast:
2	chr2:113894199..113895178-chr2:113956349..113957482,7	MCF-7	breast:
3	chr2:113895684..113896622-chr2:113956462..113957445,3	MCF-7	breast:
4	chr2:113956422..113958569-chr2:113991553..113994219,2	MCF-7	breast:
5	chr2:113949542..113953586-chr2:113955251..113958622,5	MCF-7	breast:
6	chr2:113895331..113896490-chr2:113956383..113957293,5	MCF-7	breast:
7	chr2:113956911..113959239-chr2:113960727..113963043,2	MCF-7	breast:
8	chr2:113956459..113959352-chr2:113984317..113985947,2	K562	blood:
9	chr2:113956609..113958908-chr2:113996941..113999634,4	MCF-7	breast:
10	chr2:113837862..113838404-chr2:113956604..113957377,3	MCF-7	breast:
11	chr2:113955248..113957880-chr2:113994557..113996875,2	MCF-7	breast:
12	chr2:113927356..113929479-chr2:113956960..113958587,2	MCF-7	breast:
13	chr2:113933537..113935192-chr2:113956517..113958039,2	MCF-7	breast:
14	chr2:113947298..113949233-chr2:113956219..113958532,2	MCF-7	breast:
15	chr2:113894243..113895050-chr2:113956611..113957124,2	MCF-7	breast:
16	chr2:113912322..113918193-chr2:113953978..113958305,10	MCF-7	breast:
17	chr2:113913769..113918338-chr2:113954843..113958220,11	MCF-7	breast:
18	chr2:113837234..113838476-chr2:113956411..113957308,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258395	Chromatin interaction
ENSG00000189223	Chromatin interaction
ENSG00000234174	Chromatin interaction
ENSG00000125618	Chromatin interaction
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10175462	0.82[ASN][1000 genomes]
rs10206269	0.81[ASN][1000 genomes]
rs1110839	0.81[ASN][1000 genomes]
rs11123170	0.82[ASN][1000 genomes]
rs11123172	0.82[ASN][1000 genomes]
rs12619508	0.84[EUR][1000 genomes]
rs12620738	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2015769	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2019137	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305133	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2863243	0.82[ASN][1000 genomes]
rs3748916	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3811059	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3828188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4848318	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849169	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4849176	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4849177	0.81[ASN][1000 genomes]
rs4849179	0.82[ASN][1000 genomes]
rs4849183	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62160781	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6707386	0.82[ASN][1000 genomes]
rs6755040	0.82[ASN][1000 genomes]
rs6755639	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs731834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7421852	0.81[ASN][1000 genomes]
rs7563094	0.82[ASN][1000 genomes]
rs7578633	0.82[ASN][1000 genomes]
rs895412	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs902695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs902696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874899	chr2:113935407-113962071	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874900	chr2:113948378-113967990	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12612729	PAX8	cis	Adipose Subcutaneous	GTEx
rs12612729	PAX8	cis	Esophagus Muscularis	GTEx
rs12612729	AC016683.6	cis	Esophagus Mucosa	GTEx
rs12612729	AC016683.6	cis	lung	GTEx
rs12612729	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs12612729	PAX8	cis	Esophagus Mucosa	GTEx
rs12612729	AC016683.6	cis	Esophagus Muscularis	GTEx
rs12612729	AC016683.6	cis	Muscle Skeletal	GTEx
rs12612729	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs12612729	AC016683.6	cis	Whole Blood	GTEx
rs12612729	PAX8	cis	lung	GTEx
rs12612729	AC016683.6	cis	Nerve Tibial	GTEx
rs12612729	AC016683.6	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113940000-113961000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr2:113942800-113961000	Strong transcription	Dnd41	blood
3	chr2:113947400-113961000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr2:113947800-113959600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:113947800-113960600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:113948600-113961000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:113949000-113961200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:113950000-113961000	Strong transcription	Primary T cells from cord blood	blood
9	chr2:113952600-113957800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:113955800-113957200	Weak transcription	Primary B cells from cord blood	blood
11	chr2:113955800-113957600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:113955800-113958000	Weak transcription	K562	blood
13	chr2:113955800-113959200	Enhancers	Stomach Mucosa	stomach
14	chr2:113956000-113957200	Active TSS	H1 Cell Line	embryonic stem cell
15	chr2:113956000-113957200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr2:113956000-113957200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:113956000-113957200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:113956000-113957200	Active TSS	Colonic Mucosa	Colon
19	chr2:113956000-113957200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr2:113956000-113957200	Active TSS	Pancreas	Pancrea
21	chr2:113956000-113957400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:113956000-113957800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:113956000-113958200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:113956200-113957200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr2:113956200-113957200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:113956200-113957200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:113956200-113957200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:113956200-113957200	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr2:113956200-113957200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:113956200-113957200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:113956200-113957200	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr2:113956200-113957200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr2:113956200-113957200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr2:113956200-113957200	Active TSS	Brain Germinal Matrix	brain
35	chr2:113956200-113957200	Active TSS	Brain Substantia Nigra	brain
36	chr2:113956200-113957200	Active TSS	Colon Smooth Muscle	Colon
37	chr2:113956200-113957200	Active TSS	Fetal Intestine Large	intestine
38	chr2:113956200-113957200	Active TSS	Fetal Kidney	kidney
39	chr2:113956200-113957200	Active TSS	Gastric	stomach
40	chr2:113956200-113957200	Active TSS	Ovary	ovary
41	chr2:113956200-113957200	Active TSS	Psoas Muscle	Psoas
42	chr2:113956200-113957200	Active TSS	Rectal Smooth Muscle	rectum
43	chr2:113956200-113957200	Active TSS	Right Atrium	heart
44	chr2:113956200-113957200	Active TSS	NHDF-Ad	bronchial
45	chr2:113956200-113957400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:113956200-113957400	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr2:113956200-113957400	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr2:113956200-113957400	Active TSS	Fetal Brain Female	brain
49	chr2:113956200-113957400	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr2:113956200-113957400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

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