Variant report

Variant	rs34401389
Chromosome Location	chr17:19989436-19989437
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:19989367-19989598	MCF-7	breast:	n/a	n/a
2	CTCF	chr17:19989431-19989487	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19880813..19883681-chr17:19988880..19990706,2	MCF-7	breast:

Variant related genes	Relation type
SPECC1	TF binding region
ENSG00000108599	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10083856	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1034904	0.81[AMR][1000 genomes]
rs11867585	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868084	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11868116	0.83[EUR][1000 genomes]
rs11869616	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11870111	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11871651	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936443	0.83[EUR][1000 genomes]
rs16960697	0.83[EUR][1000 genomes]
rs1859407	0.81[EUR][1000 genomes]
rs2013443	0.83[EUR][1000 genomes]
rs2042046	0.83[EUR][1000 genomes]
rs2107565	0.80[EUR][1000 genomes]
rs2108980	0.81[AMR][1000 genomes]
rs2189709	0.81[EUR][1000 genomes]
rs2526463	0.81[EUR][1000 genomes]
rs2703795	0.81[EUR][1000 genomes]
rs2703800	0.80[EUR][1000 genomes]
rs28603224	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28637614	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28666381	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28807825	0.83[AMR][1000 genomes]
rs34290687	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35003563	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35313716	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36077949	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3862152	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3888318	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3909258	0.83[AMR][1000 genomes]
rs4005937	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4267380	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4479309	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4570919	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4924801	0.81[AMR][1000 genomes]
rs4924803	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924806	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925065	0.81[AMR][1000 genomes]
rs4925066	0.81[AMR][1000 genomes]
rs4925067	0.81[AMR][1000 genomes]
rs4925069	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4925072	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4925073	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4925077	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925079	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925081	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925085	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925086	0.83[EUR][1000 genomes]
rs4925087	0.83[EUR][1000 genomes]
rs4925090	0.81[EUR][1000 genomes]
rs4925091	0.81[EUR][1000 genomes]
rs55705283	0.83[EUR][1000 genomes]
rs62066865	0.83[EUR][1000 genomes]
rs62066870	0.81[EUR][1000 genomes]
rs62067555	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587219	0.83[EUR][1000 genomes]
rs7207625	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7208025	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208365	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208635	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7209734	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7212500	0.82[EUR][1000 genomes]
rs7216599	0.82[EUR][1000 genomes]
rs7216794	0.82[EUR][1000 genomes]
rs7219908	0.82[EUR][1000 genomes]
rs7222984	0.83[EUR][1000 genomes]
rs7222987	0.81[EUR][1000 genomes]
rs7223305	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065337	0.80[AMR][1000 genomes]
rs8066143	0.82[EUR][1000 genomes]
rs8078716	0.82[EUR][1000 genomes]
rs8080649	0.81[EUR][1000 genomes]
rs888423	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs918227	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs918228	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9889743	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9891739	0.83[AMR][1000 genomes]
rs9893832	0.82[EUR][1000 genomes]
rs9896411	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897246	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9897653	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9898080	0.83[EUR][1000 genomes]
rs9901336	0.81[EUR][1000 genomes]
rs9901796	0.81[EUR][1000 genomes]
rs9902032	0.83[EUR][1000 genomes]
rs9907788	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9912775	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915758	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9944451	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv907872	chr17:19945841-19996140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1056224	chr17:19946604-19993026	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv543258	chr17:19946604-19993026	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	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
13	esv2762522	chr17:19976462-19996429	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34401389	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19977600-19989600	Weak transcription	K562	blood
2	chr17:19978800-20000000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr17:19980600-19994600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr17:19980800-19990000	Weak transcription	A549	lung
5	chr17:19981200-19993000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr17:19982600-19993000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr17:19983200-19993400	Weak transcription	Spleen	Spleen
8	chr17:19985600-19993000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr17:19986200-19993000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:19986400-19990600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr17:19986400-19991400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr17:19987000-19994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr17:19987800-19990200	Enhancers	NHDF-Ad	bronchial
14	chr17:19988000-19990200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:19988000-19990200	Enhancers	Ovary	ovary
16	chr17:19988000-19991200	Enhancers	Brain Angular Gyrus	brain
17	chr17:19988200-19989600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr17:19988200-19989600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr17:19988200-19990000	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr17:19988200-19990200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:19988200-19990200	Enhancers	Brain Anterior Caudate	brain
22	chr17:19988200-19990200	Enhancers	Brain Hippocampus Middle	brain
23	chr17:19988200-19990200	Enhancers	Brain Substantia Nigra	brain
24	chr17:19988200-19990200	Enhancers	Left Ventricle	heart
25	chr17:19988200-19990200	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr17:19988200-19990200	Enhancers	NH-A	brain
27	chr17:19988200-19990400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr17:19988200-19990400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr17:19988200-19990400	Enhancers	Fetal Muscle Trunk	muscle
30	chr17:19988200-19990600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr17:19988200-19991000	Enhancers	HSMMtube	muscle
32	chr17:19988200-19991200	Enhancers	Adipose Nuclei	Adipose
33	chr17:19988200-19991200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr17:19988400-19989600	Enhancers	HSMM	muscle
35	chr17:19988400-19989800	Genic enhancers	Monocytes-CD14+_RO01746	blood
36	chr17:19988400-19990200	Enhancers	Esophagus	oesophagus
37	chr17:19988400-19990400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr17:19988600-19990000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr17:19988600-19990200	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr17:19988600-19993200	Weak transcription	GM12878-XiMat	blood
41	chr17:19988600-19994600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr17:19988800-19989600	Enhancers	Fetal Brain Male	brain
43	chr17:19988800-19991400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr17:19988800-19994600	Weak transcription	Right Atrium	heart
45	chr17:19989000-19989800	Enhancers	Placenta	Placenta
46	chr17:19989000-19990400	Enhancers	Brain Cingulate Gyrus	brain
47	chr17:19989000-19994600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr17:19989200-19989600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr17:19989200-19989800	Enhancers	Placenta Amnion	Placenta Amnion
50	chr17:19989200-19990200	Enhancers	Aorta	Aorta

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