Variant report

Variant	rs12460461
Chromosome Location	chr19:42277077-42277078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42274897..42278651-chr19:42287593..42289573,3	MCF-7	breast:
2	chr19:42262778..42266389-chr19:42276917..42279036,3	MCF-7	breast:
3	chr19:42252191..42260165-chr19:42275924..42285275,20	MCF-7	breast:
4	chr19:42208175..42212316-chr19:42277076..42281781,5	MCF-7	breast:
5	chr19:42271676..42273430-chr19:42276461..42278418,2	MCF-7	breast:
6	chr19:42250551..42264892-chr19:42273965..42282481,23	MCF-7	breast:

Variant related genes	Relation type
ENSG00000007306	Chromatin interaction
ENSG00000086548	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10403840	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10408842	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10409763	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10413359	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10418434	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11548735	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12460493	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1971787	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2116943	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2701	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28547939	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6508997	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7258008	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8104232	0.84[EUR][1000 genomes]
rs8105477	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8106277	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv579615	chr19:42221434-42310388	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv3430577	chr19:42247653-42285973	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv911774	chr19:42250325-42288821	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3384883	chr19:42253458-42288853	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3319044	chr19:42257039-42297123	Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3319045	chr19:42257039-42297123	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2763205	chr19:42258547-42290598	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv911775	chr19:42259228-42288821	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42263400-42277800	Weak transcription	Esophagus	oesophagus
2	chr19:42274800-42281400	Enhancers	Fetal Intestine Small	intestine
3	chr19:42275200-42277600	Weak transcription	Colonic Mucosa	Colon
4	chr19:42275200-42281000	Enhancers	Fetal Intestine Large	intestine
5	chr19:42276000-42278200	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr19:42276000-42279800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr19:42276200-42278200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:42276200-42278400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr19:42276200-42278400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr19:42276200-42278400	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr19:42276200-42278600	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr19:42276200-42279600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr19:42276200-42282400	Enhancers	Stomach Mucosa	stomach
14	chr19:42276400-42278000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr19:42276400-42278200	Enhancers	Primary T cells from cord blood	blood
16	chr19:42276600-42278000	Enhancers	Small Intestine	intestine
17	chr19:42276600-42278400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:42276800-42277200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr19:42276800-42277200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr19:42276800-42277600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr19:42276800-42278000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:42276800-42279000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr19:42276800-42280000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:42276800-42282200	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr19:42277000-42279800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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