Variant report

Variant	rs4667040
Chromosome Location	chr2:186341789-186341790
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	chr2:186334605..186336794-chr2:186340639..186343119,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10196025	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10199557	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10206949	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10210704	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10803985	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931174	0.85[EUR][1000 genomes]
rs10931175	0.84[EUR][1000 genomes]
rs10931188	0.84[EUR][1000 genomes]
rs11886336	0.84[EUR][1000 genomes]
rs12105970	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12478484	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12990307	0.81[EUR][1000 genomes]
rs13018197	0.80[EUR][1000 genomes]
rs13384417	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13393941	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1424542	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1477454	0.82[EUR][1000 genomes]
rs16826958	0.83[EUR][1000 genomes]
rs2042507	0.82[EUR][1000 genomes]
rs2111711	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2216402	0.84[EUR][1000 genomes]
rs2370390	0.84[EUR][1000 genomes]
rs4233785	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4300794	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4306683	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4319900	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4377305	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4549042	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4666688	0.84[EUR][1000 genomes]
rs4667044	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4667045	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4667047	0.84[EUR][1000 genomes]
rs6434134	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67102416	0.80[EUR][1000 genomes]
rs6729201	0.81[EUR][1000 genomes]
rs6737269	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6745292	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6747256	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6749577	0.82[EUR][1000 genomes]
rs6753011	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7560513	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7577958	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7593254	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7599179	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7601391	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584009	chr2:186203397-186345148	Active TSS Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv459983	chr2:186245653-186377253	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv584013	chr2:186245653-186377253	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	nsv1009994	chr2:186308867-186370097	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
20	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
21	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
22	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
23	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
24	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
25	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
26	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4667040	AC007966.1	cis	Adipose Subcutaneous	GTEx
rs4667040	AC007966.1	cis	Thyroid	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:186314400-186345200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:186321400-186358600	Weak transcription	HMEC	breast
3	chr2:186331800-186342000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:186339200-186347600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:186339200-186358400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:186339200-186358400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:186340600-186343800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr2:186340800-186342200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr2:186340800-186342200	Enhancers	H9 Cell Line	embryonic stem cell
10	chr2:186340800-186342200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr2:186340800-186344000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr2:186341000-186342000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr2:186341000-186343800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr2:186341200-186343000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:186341200-186349600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:186341400-186341800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:186341400-186342400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr2:186341600-186342000	Weak transcription	H1 Cell Line	embryonic stem cell

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