Variant report

Variant	rs12080246
Chromosome Location	chr1:228700398-228700399
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228699934-228701457	PBDE	blood:	n/a	n/a
2	GATA1	chr1:228699888-228703545	K562	blood:	n/a	chr1:228701158-228701168

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228638761..228647671-chr1:228695176..228704605,18	K562	blood:
2	chr1:228677727..228683972-chr1:228696742..228702359,8	K562	blood:
3	chr1:228268869..228271597-chr1:228699816..228701498,2	K562	blood:
4	chr1:228643550..228646999-chr1:228697754..228701028,5	K562	blood:
5	chr1:228674158..228676652-chr1:228698714..228701340,3	K562	blood:
6	chr1:228353428..228355083-chr1:228698397..228701080,2	K562	blood:
7	chr1:228594895..228597342-chr1:228698615..228701560,2	K562	blood:
8	chr1:228675436..228678007-chr1:228697619..228700594,3	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
BTNL10	TF binding region
ENSG00000231563	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000168159	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10916330	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10916334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060613	0.91[ASN][1000 genomes]
rs12063103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12066593	0.83[ASN][1000 genomes]
rs12068246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12072917	0.91[ASN][1000 genomes]
rs12072922	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12084511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3795818	1.00[JPT][hapmap]
rs4436391	1.00[JPT][hapmap]
rs4653951	1.00[YRI][hapmap]
rs61827301	0.83[ASN][1000 genomes]
rs61827303	0.91[ASN][1000 genomes]
rs61827304	0.91[ASN][1000 genomes]
rs6683136	1.00[JPT][hapmap]
rs72763967	0.91[ASN][1000 genomes]
rs72763981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
5	nsv549297	chr1:228681195-228720480	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv468305	chr1:228681195-228731677	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv549298	chr1:228681195-228731677	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv947521	chr1:228698244-228704499	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228696800-228700400	Enhancers	K562	blood
2	chr1:228697600-228702400	Weak transcription	Esophagus	oesophagus
3	chr1:228699000-228700400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:228699000-228702600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:228699200-228701400	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr1:228699400-228700800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:228699600-228701400	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr1:228699800-228701400	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr1:228699800-228701600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:228700200-228700800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:228700200-228701000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:228700200-228701200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:228700200-228701400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
14	chr1:228700200-228701400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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