Variant report

Variant	rs12713794
Chromosome Location	chr2:73956846-73956847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73940417..73941921-chr2:73955171..73957279,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10172044	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10191988	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10193032	0.85[ASN][1000 genomes]
rs10200762	0.86[AMR][1000 genomes]
rs10203740	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10208995	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11126414	0.84[EUR][1000 genomes]
rs11126415	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11126416	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11126417	0.89[EUR][1000 genomes]
rs11891140	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11892172	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11894953	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12052539	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12053242	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12233112	0.84[EUR][1000 genomes]
rs12233115	0.84[EUR][1000 genomes]
rs12611487	0.82[EUR][1000 genomes]
rs12612423	0.82[EUR][1000 genomes]
rs12615807	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12619258	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12624267	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12713788	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12713789	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12713790	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12713791	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12713793	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12713795	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12713797	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12713798	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12992607	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997568	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12998980	0.83[EUR][1000 genomes]
rs13000788	0.82[EUR][1000 genomes]
rs13003035	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13005729	0.84[EUR][1000 genomes]
rs13006448	0.84[EUR][1000 genomes]
rs13006598	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13013228	0.84[EUR][1000 genomes]
rs13014700	0.83[EUR][1000 genomes]
rs13015885	0.83[EUR][1000 genomes]
rs13020517	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13031853	0.84[EUR][1000 genomes]
rs13031866	0.84[EUR][1000 genomes]
rs13033744	0.83[EUR][1000 genomes]
rs13383097	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17350056	0.84[EUR][1000 genomes]
rs17350125	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17350188	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17434634	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17434655	0.84[EUR][1000 genomes]
rs1806683	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1815028	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2001436	0.84[EUR][1000 genomes]
rs2001490	0.84[EUR][1000 genomes]
rs2006997	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2012574	0.84[EUR][1000 genomes]
rs2116367	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2272051	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2272178	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2421557	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2421558	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2421559	0.87[EUR][1000 genomes]
rs2421575	0.83[EUR][1000 genomes]
rs2421672	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2421674	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2421675	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2421676	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2421677	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2462127	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35498419	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35528262	0.82[EUR][1000 genomes]
rs35767294	0.84[EUR][1000 genomes]
rs35791379	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3813228	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3980695	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4241257	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4358149	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4513320	0.84[EUR][1000 genomes]
rs4530394	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4852316	0.89[EUR][1000 genomes]
rs4852972	0.82[EUR][1000 genomes]
rs4852975	0.84[EUR][1000 genomes]
rs4852976	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4852977	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4852978	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6732812	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6748233	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6749841	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6750494	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6750515	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6750877	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6755500	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7210	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732778	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7370393	0.84[EUR][1000 genomes]
rs7558546	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7591112	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7597302	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7599453	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs891695	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs891696	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9309475	0.90[EUR][1000 genomes]
rs9309476	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1013385	chr2:73822056-74041441	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv874276	chr2:73847024-73964214	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	9 gene(s)	inside rSNPs	diseases
6	nsv834260	chr2:73906106-74076520	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv998315	chr2:73919185-74003998	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1000675	chr2:73919185-74038946	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1003153	chr2:73927235-73975416	Weak transcription Flanking Active TSS Enhancers 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	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12713794	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs12713794	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73944000-73958000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:73944400-73958000	Weak transcription	Osteobl	bone
3	chr2:73944600-73963000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:73944600-73963600	Weak transcription	Stomach Mucosa	stomach
5	chr2:73951600-73957600	Weak transcription	K562	blood
6	chr2:73952200-73958000	Weak transcription	HUVEC	blood vessel
7	chr2:73952200-73958400	Weak transcription	NHDF-Ad	bronchial
8	chr2:73953200-73957200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:73953200-73957400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:73953200-73957800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:73953200-73959400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:73953200-73963600	Weak transcription	Small Intestine	intestine
13	chr2:73953400-73957000	Weak transcription	Hela-S3	cervix
14	chr2:73953400-73958000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:73953400-73958000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr2:73953400-73958000	Weak transcription	NHLF	lung
17	chr2:73953600-73957800	Weak transcription	Fetal Lung	lung
18	chr2:73953800-73957200	Weak transcription	NH-A	brain
19	chr2:73953800-73957600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:73954000-73963000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:73954200-73957600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr2:73954200-73958000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:73954200-73958200	Weak transcription	Psoas Muscle	Psoas
24	chr2:73954400-73958000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:73954600-73958600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr2:73954600-73961400	Strong transcription	Primary T cells from cord blood	blood
27	chr2:73954600-73962000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:73954600-73963600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr2:73954800-73957800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:73954800-73961000	Strong transcription	A549	lung
31	chr2:73954800-73962000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:73954800-73962000	Strong transcription	Fetal Stomach	stomach
33	chr2:73954800-73962200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:73954800-73962200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:73955000-73957000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:73955000-73960800	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:73955000-73961000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:73955000-73961000	Strong transcription	Adipose Nuclei	Adipose
39	chr2:73955000-73961200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:73955000-73961800	Strong transcription	Liver	Liver
41	chr2:73955000-73961800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:73955000-73961800	Strong transcription	Dnd41	blood
43	chr2:73955000-73962000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:73955000-73962000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:73955000-73962000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr2:73955000-73962000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr2:73955000-73962000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:73955000-73962000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:73955000-73962000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr2:73955000-73962000	Strong transcription	Monocytes-CD14+_RO01746	blood

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