Variant report

Variant	rs12647830
Chromosome Location	chr4:99065780-99065781
allele	G/T
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	POLR2A	chr4:99063777-99065872	GM12891	blood:	n/a	n/a
2	POLR2A	chr4:99063780-99065960	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr4:99063596-99066015	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:99063959..99066263-chr4:99181971..99183968,2	K562	blood:
2	chr4:99064473..99066402-chr4:99398593..99401325,2	MCF-7	breast:
3	chr4:99062262..99068404-chr4:99178848..99183768,9	MCF-7	breast:
4	chr20:56285284..56287699-chr4:99065164..99066706,2	MCF-7	breast:

Variant related genes	Relation type
STPG2	TF binding region
ENSG00000138698	Chromatin interaction
ENSG00000124225	Chromatin interaction
ENSG00000214559	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1084778	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1084779	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1214993	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12648163	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1527514	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72686496	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs783919	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs783920	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs783926	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs783927	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs783935	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs783944	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs783946	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs783948	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs783953	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs783954	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs783956	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002098	chr4:98501337-99086320	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv537193	chr4:98501337-99086320	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv879648	chr4:98547717-99104879	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1000011	chr4:98562308-99101692	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1000956	chr4:98732458-99178588	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1001570	chr4:98976239-99239838	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv879650	chr4:99057457-99172232	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv998270	chr4:99063275-99120404	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv461595	chr4:99065480-99172175	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv594939	chr4:99065480-99172175	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99065000-99067200	Weak transcription	NHDF-Ad	bronchial
2	chr4:99065200-99065800	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr4:99065200-99069000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr4:99065200-99069400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr4:99065200-99069600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr4:99065200-99069600	Weak transcription	HSMM	muscle
7	chr4:99065200-99069600	Weak transcription	HUVEC	blood vessel
8	chr4:99065200-99069800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:99065200-99070000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:99065200-99070000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr4:99065400-99069200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:99065400-99069200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr4:99065400-99069600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr4:99065400-99069800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr4:99065400-99069800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:99065400-99070000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:99065400-99070000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:99065600-99069400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr4:99065600-99069800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr4:99065600-99069800	Weak transcription	Primary T cells from cord blood	blood
21	chr4:99065600-99070000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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