Variant report

Variant	rs10180772
Chromosome Location	chr2:186388059-186388060
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:186387075..186388294-chr2:186603348..186604298,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188738	Chromatin interaction
ENSG00000226747	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10174315	0.85[EUR][1000 genomes]
rs10186909	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10189129	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10190576	0.85[EUR][1000 genomes]
rs10209067	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10490389	0.84[EUR][1000 genomes]
rs1075257	0.84[EUR][1000 genomes]
rs11682752	0.83[EUR][1000 genomes]
rs11684181	0.82[EUR][1000 genomes]
rs11686533	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11694100	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891430	0.90[EUR][1000 genomes]
rs11891748	0.90[EUR][1000 genomes]
rs12328928	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12328996	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13410805	0.84[EUR][1000 genomes]
rs13412749	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13421326	0.85[EUR][1000 genomes]
rs13421575	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17813140	0.85[EUR][1000 genomes]
rs28508191	0.87[EUR][1000 genomes]
rs35119381	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35379699	0.83[EUR][1000 genomes]
rs56266442	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59153366	0.83[EUR][1000 genomes]
rs59486260	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6713671	0.83[EUR][1000 genomes]
rs6716541	0.83[EUR][1000 genomes]
rs6749407	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6753178	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6755533	0.90[EUR][1000 genomes]
rs6761099	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72894199	0.85[EUR][1000 genomes]
rs72896010	0.84[EUR][1000 genomes]
rs72896445	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72896480	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593451	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7606908	0.85[EUR][1000 genomes]
rs918229	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv459982	chr2:186213755-186475590	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv584012	chr2:186213755-186475590	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv875525	chr2:186223503-186434458	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv875526	chr2:186272059-186434458	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv875527	chr2:186272059-186475590	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv459985	chr2:186293335-186422662	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv584014	chr2:186293335-186422662	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv459986	chr2:186297074-186413124	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv584015	chr2:186297074-186413124	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv584016	chr2:186301351-186410869	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv875528	chr2:186301351-186475590	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1004048	chr2:186303297-186541503	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv875529	chr2:186303530-186434458	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv875530	chr2:186303530-186475590	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv875531	chr2:186303530-186489537	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv997498	chr2:186308867-186391490	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv875532	chr2:186309738-186422662	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv875533	chr2:186309738-186433551	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv875535	chr2:186309738-186458903	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv875534	chr2:186309738-186475590	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv875536	chr2:186309738-186504175	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv875537	chr2:186336529-186422662	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv875538	chr2:186345148-186434458	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv875539	chr2:186345148-186475590	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv875540	chr2:186345148-186583961	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	nsv875541	chr2:186345148-186598526	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	nsv1006219	chr2:186352780-186524793	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
28	nsv584017	chr2:186352959-186515328	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
29	nsv584018	chr2:186352959-186598526	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
30	nsv916442	chr2:186356363-186534152	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
31	nsv875542	chr2:186358877-186422662	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
32	nsv875543	chr2:186365918-186489537	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10180772	PART1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:186359800-186393400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:186381200-186393800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:186381400-186432400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:186388000-186388200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:186388000-186388600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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