Variant report

Variant	rs12451216
Chromosome Location	chr17:20025840-20025841
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20025221..20027004-chr17:20127712..20130710,2	MCF-7	breast:
2	chr17:20025057..20027504-chr17:20071007..20074000,2	MCF-7	breast:
3	chr17:20025519..20027305-chr17:20058303..20059894,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 153 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs11204422	0.92[ASN][1000 genomes]
rs11654025	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11869931	0.92[ASN][1000 genomes]
rs11870147	0.84[EUR][1000 genomes]
rs11870381	0.86[ASN][1000 genomes]
rs11870673	0.83[ASN][1000 genomes]
rs11871827	0.84[EUR][1000 genomes]
rs11871945	0.84[EUR][1000 genomes]
rs12451841	0.93[ASN][1000 genomes]
rs12453332	0.88[ASN][1000 genomes]
rs12937827	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12941200	0.80[AMR][1000 genomes]
rs12942179	0.92[ASN][1000 genomes]
rs12947713	0.92[ASN][1000 genomes]
rs12948178	0.80[AMR][1000 genomes]
rs12949485	0.82[AMR][1000 genomes]
rs12949710	0.92[ASN][1000 genomes]
rs12952398	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1373147	0.84[EUR][1000 genomes]
rs1468953	0.92[ASN][1000 genomes]
rs1544421	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1561974	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17685923	0.92[ASN][1000 genomes]
rs17686622	0.80[AMR][1000 genomes]
rs17686798	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17686839	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17759923	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17759959	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1812934	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1985810	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1992562	0.84[EUR][1000 genomes]
rs2005722	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2013441	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2013576	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2034109	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2080673	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2107566	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2120282	0.84[EUR][1000 genomes]
rs2158473	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2165897	0.84[EUR][1000 genomes]
rs2189710	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2243732	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2263175	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2386429	0.84[EUR][1000 genomes]
rs2386485	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526458	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526460	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526462	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2526464	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2526467	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2526472	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526474	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526475	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526480	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2526483	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2526484	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2526488	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526490	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2703772	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703774	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703778	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703780	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703782	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703785	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703787	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2703789	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703790	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703791	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2703792	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2703794	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2703799	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2703801	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2703802	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2703804	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2703806	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2703808	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703810	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2703815	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703816	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703817	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703818	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703820	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703821	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34089239	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34370440	0.93[ASN][1000 genomes]
rs34644796	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34712254	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34756775	0.92[ASN][1000 genomes]
rs35041742	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35124809	0.92[ASN][1000 genomes]
rs35156798	0.88[ASN][1000 genomes]
rs35191778	0.92[ASN][1000 genomes]
rs35244101	0.92[ASN][1000 genomes]
rs35493088	0.92[ASN][1000 genomes]
rs35770292	0.89[ASN][1000 genomes]
rs36051592	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3850783	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3850784	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3850785	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3940274	0.80[ASN][1000 genomes]
rs4341795	0.92[ASN][1000 genomes]
rs4346259	0.92[ASN][1000 genomes]
rs4350625	0.92[ASN][1000 genomes]
rs4471741	0.92[ASN][1000 genomes]
rs4588033	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924808	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924809	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924810	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4925075	0.92[ASN][1000 genomes]
rs4925076	0.92[ASN][1000 genomes]
rs4925078	0.92[ASN][1000 genomes]
rs4925082	0.90[ASN][1000 genomes]
rs4925088	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4925089	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57146223	0.88[ASN][1000 genomes]
rs62067488	0.92[ASN][1000 genomes]
rs62067558	0.82[AMR][1000 genomes]
rs6587063	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7207611	0.84[EUR][1000 genomes]
rs7215803	0.92[ASN][1000 genomes]
rs7225249	0.85[ASN][1000 genomes]
rs7503407	0.92[ASN][1000 genomes]
rs8066705	0.86[ASN][1000 genomes]
rs8068484	0.90[ASN][1000 genomes]
rs8071665	0.84[EUR][1000 genomes]
rs8074047	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8074791	0.86[ASN][1000 genomes]
rs8075343	0.92[ASN][1000 genomes]
rs8079701	0.84[EUR][1000 genomes]
rs8081817	0.92[ASN][1000 genomes]
rs888424	0.92[ASN][1000 genomes]
rs9325894	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs972966	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9892630	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9896221	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9896709	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9897328	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9900166	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9901125	0.93[ASN][1000 genomes]
rs9904928	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9905493	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9915059	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9915628	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	nsv482830	chr17:20012748-20169153	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12451216	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19999000-20032800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr17:20002200-20033400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr17:20014600-20028800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:20016000-20028800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:20016400-20028600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr17:20017400-20026200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr17:20023600-20026000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr17:20023600-20026600	Enhancers	Fetal Brain Male	brain
9	chr17:20023800-20026000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr17:20024000-20026000	Enhancers	Fetal Muscle Leg	muscle
11	chr17:20024200-20026000	Enhancers	Fetal Brain Female	brain
12	chr17:20024200-20026200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr17:20024400-20026200	Enhancers	HSMM	muscle
14	chr17:20024600-20028800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr17:20024800-20026200	Enhancers	Aorta	Aorta
16	chr17:20025000-20026000	Enhancers	Fetal Stomach	stomach
17	chr17:20025000-20026000	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr17:20025000-20026400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr17:20025200-20026000	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr17:20025200-20026000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
21	chr17:20025200-20026000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr17:20025200-20026000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr17:20025200-20026000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr17:20025200-20026000	Flanking Active TSS	Osteobl	bone
25	chr17:20025200-20026200	Flanking Active TSS	Brain Angular Gyrus	brain
26	chr17:20025200-20026200	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr17:20025200-20026200	Flanking Active TSS	Brain Substantia Nigra	brain
28	chr17:20025200-20026800	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr17:20025200-20027000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr17:20025400-20026000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr17:20025400-20026200	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr17:20025400-20028800	Weak transcription	Adipose Nuclei	Adipose
33	chr17:20025400-20040400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr17:20025600-20026000	Flanking Active TSS	Colon Smooth Muscle	Colon
35	chr17:20025600-20026800	Enhancers	HSMMtube	muscle
36	chr17:20025600-20027400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr17:20025600-20031000	Weak transcription	Left Ventricle	heart
38	chr17:20025600-20034600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr17:20025800-20026000	Active TSS	Duodenum Mucosa	Duodenum
40	chr17:20025800-20026200	Enhancers	Rectal Smooth Muscle	rectum
41	chr17:20025800-20028800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr17:20025800-20029000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr17:20025800-20029200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr17:20025800-20029800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr17:20025800-20030200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr17:20025800-20031000	Weak transcription	Hela-S3	cervix
47	chr17:20025800-20037600	Weak transcription	Ovary	ovary
48	chr17:20025800-20044400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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