Variant report

Variant	rs7222987
Chromosome Location	chr17:20055765-20055766
allele	A/G
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	STAT3	chr17:20055719-20055900	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:19993292..19995156-chr17:20055465..20057406,2	MCF-7	breast:
2	chr17:20051458..20053031-chr17:20053497..20055897,2	MCF-7	breast:
3	chr17:20041429..20043653-chr17:20055230..20057958,2	K562	blood:

Variant related genes	Relation type
SPECC1	TF binding region

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10491107	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11204300	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11204423	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11653630	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11653869	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11654942	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11657161	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11867585	0.80[EUR][1000 genomes]
rs11868116	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11869258	0.84[EUR][1000 genomes]
rs11871651	0.80[EUR][1000 genomes]
rs12603372	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12936443	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12938355	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12942568	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12942627	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12949481	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12950564	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1373146	0.84[EUR][1000 genomes]
rs16960697	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1859407	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1974745	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1992561	0.84[EUR][1000 genomes]
rs2013443	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2042046	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2107565	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2158472	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2189709	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2526459	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2526463	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2526465	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2526466	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2526476	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526477	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526478	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2526481	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2526482	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2526486	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2703770	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2703771	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2703776	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2703777	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2703781	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703786	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703788	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703795	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2703800	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2703803	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2703805	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2703807	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2703812	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2703814	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2703819	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28603224	0.80[EUR][1000 genomes]
rs28637614	0.80[EUR][1000 genomes]
rs28666381	0.80[EUR][1000 genomes]
rs34290687	0.80[EUR][1000 genomes]
rs34401389	0.81[EUR][1000 genomes]
rs35003563	0.81[EUR][1000 genomes]
rs36077949	0.80[EUR][1000 genomes]
rs3850779	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3850780	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4570919	0.80[EUR][1000 genomes]
rs4924803	0.80[EUR][1000 genomes]
rs4924806	0.81[EUR][1000 genomes]
rs4925079	0.80[EUR][1000 genomes]
rs4925085	0.80[EUR][1000 genomes]
rs4925086	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4925087	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925090	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925091	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55705283	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57837691	0.84[EUR][1000 genomes]
rs62066865	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62066870	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62067555	0.80[EUR][1000 genomes]
rs6587219	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7207625	0.80[EUR][1000 genomes]
rs7208025	0.80[EUR][1000 genomes]
rs7208365	0.80[EUR][1000 genomes]
rs7208635	0.80[EUR][1000 genomes]
rs7212500	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7212571	0.80[EUR][1000 genomes]
rs7216599	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7216794	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7219615	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7219908	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7222984	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7223305	0.80[EUR][1000 genomes]
rs733794	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs757494	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs757495	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8066143	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8071274	0.84[EUR][1000 genomes]
rs8078716	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8080649	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs888423	0.80[EUR][1000 genomes]
rs918228	0.80[EUR][1000 genomes]
rs9893832	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9896411	0.80[EUR][1000 genomes]
rs9897653	0.80[EUR][1000 genomes]
rs9898080	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9901336	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9901796	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9902032	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9907516	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9907788	0.80[EUR][1000 genomes]
rs9944451	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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
11	nsv833396	chr17:20029183-20150808	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv2003	chr17:20046306-20090653	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7222987	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20029600-20058800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:20031800-20056400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr17:20032000-20058600	Weak transcription	A549	lung
4	chr17:20042800-20058400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:20045400-20058400	Weak transcription	K562	blood
6	chr17:20047400-20058400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:20049800-20058000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr17:20052800-20056400	Weak transcription	Brain Angular Gyrus	brain
9	chr17:20052800-20057800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr17:20052800-20058800	Weak transcription	Adipose Nuclei	Adipose
11	chr17:20052800-20058800	Weak transcription	Aorta	Aorta
12	chr17:20053000-20056400	Weak transcription	Brain Hippocampus Middle	brain
13	chr17:20053000-20058400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr17:20053000-20058600	Weak transcription	Brain Substantia Nigra	brain
15	chr17:20053200-20058400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr17:20053200-20058400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr17:20054600-20058800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr17:20054800-20058400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr17:20055000-20058400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr17:20055000-20058600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:20055000-20058600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr17:20055000-20058600	Weak transcription	Monocytes-CD14+_RO01746	blood

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