Variant report

Variant	rs12460781
Chromosome Location	chr19:39085846-39085847
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39084024..39086357-chr19:39108098..39109924,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178982	Chromatin interaction
ENSG00000104814	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12460221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17847683	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17847686	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17847695	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2287736	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287737	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786852	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39053200-39086800	Weak transcription	Brain Angular Gyrus	brain
2	chr19:39053200-39086800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr19:39056400-39086400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr19:39064200-39086400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr19:39067000-39086600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:39070600-39086200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr19:39070600-39100000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:39071200-39086000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:39074800-39087000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr19:39074800-39101600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr19:39075400-39087000	Weak transcription	Colonic Mucosa	Colon
12	chr19:39076600-39089600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr19:39076600-39093200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:39076800-39092800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr19:39077000-39086000	Weak transcription	Fetal Stomach	stomach
16	chr19:39077000-39086200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:39077000-39101600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr19:39077200-39103200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr19:39077400-39086400	Weak transcription	Esophagus	oesophagus
20	chr19:39077800-39093000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:39078000-39088400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:39078000-39089000	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr19:39078000-39089200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr19:39078000-39089800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:39078200-39092200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:39078600-39086200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:39078600-39086800	Weak transcription	Brain Hippocampus Middle	brain
28	chr19:39078800-39086200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr19:39078800-39086400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:39078800-39086400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr19:39078800-39086600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr19:39078800-39086800	Weak transcription	Lung	lung
33	chr19:39078800-39086800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr19:39078800-39087000	Weak transcription	Right Atrium	heart
35	chr19:39079000-39086000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:39079000-39086200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:39079000-39086800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr19:39079000-39086800	Weak transcription	Brain Anterior Caudate	brain
39	chr19:39079200-39086400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr19:39081000-39088600	Strong transcription	Thymus	Thymus
41	chr19:39081400-39088400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr19:39081800-39087000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr19:39082600-39086400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr19:39082600-39086400	Strong transcription	Spleen	Spleen
45	chr19:39082600-39086800	Strong transcription	Primary T cells from cord blood	blood
46	chr19:39082600-39088600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr19:39083200-39086800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr19:39083400-39088600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr19:39083600-39088600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr19:39083800-39088600	Strong transcription	GM12878-XiMat	blood

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