Variant report

Variant	rs12943904
Chromosome Location	chr17:20007567-20007568
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20006703..20009085-chr17:20010910..20012831,2	K562	blood:
2	chr17:19806568..19809445-chr17:20006913..20008589,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10083830	1.00[ASN][1000 genomes]
rs10083840	1.00[ASN][1000 genomes]
rs10438824	0.80[EUR][1000 genomes]
rs11869931	0.90[AMR][1000 genomes]
rs12449914	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12453332	0.89[AMR][1000 genomes]
rs12937327	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12941200	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12947713	0.90[AMR][1000 genomes]
rs12947950	0.82[EUR][1000 genomes]
rs12948178	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12949485	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12949710	0.90[AMR][1000 genomes]
rs1468953	0.90[AMR][1000 genomes]
rs17685923	0.90[AMR][1000 genomes]
rs17686622	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17759041	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17759083	1.00[ASN][1000 genomes]
rs17759609	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703797	0.80[EUR][1000 genomes]
rs34756775	0.90[AMR][1000 genomes]
rs35124809	0.90[AMR][1000 genomes]
rs35156798	0.90[AMR][1000 genomes]
rs35191778	0.90[AMR][1000 genomes]
rs35244101	0.90[AMR][1000 genomes]
rs35317166	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35493088	0.90[AMR][1000 genomes]
rs35770292	0.90[AMR][1000 genomes]
rs35915823	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862151	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4341795	0.90[AMR][1000 genomes]
rs4346259	0.90[AMR][1000 genomes]
rs4350625	0.90[AMR][1000 genomes]
rs4471741	0.89[AMR][1000 genomes]
rs4924802	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925071	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925074	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925075	0.90[AMR][1000 genomes]
rs4925076	0.90[AMR][1000 genomes]
rs4925078	0.90[AMR][1000 genomes]
rs4925084	0.93[AMR][1000 genomes]
rs56371654	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62067488	0.90[AMR][1000 genomes]
rs62067558	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7503407	0.90[AMR][1000 genomes]
rs8068484	0.89[AMR][1000 genomes]
rs8075343	0.90[AMR][1000 genomes]
rs8081817	0.90[AMR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12943904	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19993800-20008800	Weak transcription	GM12878-XiMat	blood
2	chr17:19999000-20032800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr17:19999200-20008800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:19999400-20011800	Weak transcription	A549	lung
5	chr17:20002200-20018800	Weak transcription	Spleen	Spleen
6	chr17:20002200-20033400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr17:20002400-20013600	Weak transcription	Aorta	Aorta
8	chr17:20004000-20013600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr17:20004600-20008400	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr17:20004800-20007600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:20005000-20007600	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr17:20005000-20007800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr17:20006000-20007600	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr17:20006000-20008800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr17:20006400-20007600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:20006400-20007600	Enhancers	Brain Angular Gyrus	brain
17	chr17:20006400-20008800	Enhancers	Placenta Amnion	Placenta Amnion
18	chr17:20006600-20007800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr17:20006600-20007800	Enhancers	Brain Anterior Caudate	brain
20	chr17:20006600-20007800	Enhancers	HSMMtube	muscle
21	chr17:20006800-20008400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:20007000-20007600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr17:20007000-20007600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:20007000-20007600	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:20007000-20007600	Enhancers	Brain Cingulate Gyrus	brain
26	chr17:20007000-20007800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr17:20007000-20013400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr17:20007000-20013600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:20007200-20007600	Enhancers	Brain Substantia Nigra	brain
30	chr17:20007200-20013600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr17:20007400-20007600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr17:20007400-20007600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr17:20007400-20007600	Bivalent Enhancer	HSMM	muscle
34	chr17:20007400-20007800	Enhancers	Brain Hippocampus Middle	brain
35	chr17:20007400-20009000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr17:20007400-20013600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr17:20007400-20013600	Weak transcription	Ovary	ovary
38	chr17:20007400-20015000	Weak transcription	Adipose Nuclei	Adipose
39	chr17:20007400-20024200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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