Variant report

Variant	rs7208635
Chromosome Location	chr17:19990990-19990991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19987801..19990549-chr17:19990634..19992349,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10083856	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1034904	0.83[AMR][1000 genomes]
rs11867585	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868084	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11868116	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11869616	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11870111	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11871651	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936443	0.82[EUR][1000 genomes]
rs16960697	0.82[EUR][1000 genomes]
rs1859407	0.81[EUR][1000 genomes]
rs1860302	0.80[AMR][1000 genomes]
rs2013443	0.82[EUR][1000 genomes]
rs2042046	0.82[EUR][1000 genomes]
rs2108979	0.80[AMR][1000 genomes]
rs2108980	0.83[AMR][1000 genomes]
rs2189709	0.81[EUR][1000 genomes]
rs2526463	0.81[EUR][1000 genomes]
rs2703795	0.80[EUR][1000 genomes]
rs28603224	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28637614	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28666381	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28807825	0.85[AMR][1000 genomes]
rs34290687	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34291370	0.81[AMR][1000 genomes]
rs34401389	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35003563	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35313716	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36077949	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3862152	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3888318	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3909258	0.85[AMR][1000 genomes]
rs4005937	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4267380	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4479309	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4570919	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4924801	0.83[AMR][1000 genomes]
rs4924803	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924806	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925065	0.83[AMR][1000 genomes]
rs4925066	0.83[AMR][1000 genomes]
rs4925067	0.83[AMR][1000 genomes]
rs4925069	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4925072	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4925073	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4925077	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925079	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925081	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925085	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925086	0.82[EUR][1000 genomes]
rs4925087	0.82[EUR][1000 genomes]
rs4925090	0.80[EUR][1000 genomes]
rs4925091	0.80[EUR][1000 genomes]
rs55705283	0.82[EUR][1000 genomes]
rs62066865	0.82[EUR][1000 genomes]
rs62066870	0.80[EUR][1000 genomes]
rs62067555	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587219	0.82[EUR][1000 genomes]
rs7207625	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7208025	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208365	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7209734	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7211535	0.80[AMR][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	0.80[EUR][1000 genomes]
rs7223305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065337	0.82[AMR][1000 genomes]
rs8066143	0.82[EUR][1000 genomes]
rs8067545	0.81[AMR][1000 genomes]
rs8078716	0.82[EUR][1000 genomes]
rs8080649	0.80[EUR][1000 genomes]
rs888423	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs918227	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs918228	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9889743	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9891739	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9893832	0.82[EUR][1000 genomes]
rs9896411	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9897246	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9897653	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9898080	0.82[EUR][1000 genomes]
rs9901336	0.80[EUR][1000 genomes]
rs9901796	0.80[EUR][1000 genomes]
rs9902032	0.83[EUR][1000 genomes]
rs9907788	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9912775	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915758	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9944451	0.98[AMR][1000 genomes];0.99[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
rs7208635	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19978800-20000000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:19980600-19994600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr17:19981200-19993000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr17:19982600-19993000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr17:19983200-19993400	Weak transcription	Spleen	Spleen
6	chr17:19985600-19993000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr17:19986200-19993000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:19986400-19991400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:19987000-19994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr17:19988000-19991200	Enhancers	Brain Angular Gyrus	brain
11	chr17:19988200-19991000	Enhancers	HSMMtube	muscle
12	chr17:19988200-19991200	Enhancers	Adipose Nuclei	Adipose
13	chr17:19988200-19991200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr17:19988600-19993200	Weak transcription	GM12878-XiMat	blood
15	chr17:19988600-19994600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr17:19988800-19991400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr17:19988800-19994600	Weak transcription	Right Atrium	heart
18	chr17:19989000-19994600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr17:19989200-19991600	Enhancers	Fetal Muscle Leg	muscle
20	chr17:19989200-19994200	Weak transcription	Osteobl	bone
21	chr17:19989400-19994200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr17:19989600-19991200	Enhancers	Stomach Mucosa	stomach
23	chr17:19989600-19994000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr17:19989800-19992400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr17:19990000-19991200	Enhancers	A549	lung
26	chr17:19990000-19993000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr17:19990000-19995600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr17:19990200-19991200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr17:19990200-19991800	Weak transcription	Aorta	Aorta
30	chr17:19990200-19992200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:19990200-19993000	Weak transcription	Left Ventricle	heart
32	chr17:19990200-19993400	Weak transcription	Esophagus	oesophagus
33	chr17:19990200-19993600	Weak transcription	NHDF-Ad	bronchial
34	chr17:19990200-19994000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr17:19990200-19994000	Weak transcription	Ovary	ovary
36	chr17:19990200-19994000	Weak transcription	Right Ventricle	heart
37	chr17:19990200-19994000	Weak transcription	NH-A	brain
38	chr17:19990200-19994600	Weak transcription	Brain Anterior Caudate	brain
39	chr17:19990200-19994600	Weak transcription	Brain Hippocampus Middle	brain
40	chr17:19990200-19994600	Weak transcription	Brain Substantia Nigra	brain
41	chr17:19990200-19994800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr17:19990200-19995000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr17:19990200-19998800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr17:19990400-19991000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr17:19990400-19994600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr17:19990400-19994600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr17:19990600-19994000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:19990600-19995000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr17:19990800-19991600	Enhancers	Placenta Amnion	Placenta Amnion

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