Variant report

Variant	rs3087453
Chromosome Location	chr19:41860934-41860935
allele	C/G
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	CTCF	chr19:41856797-41862442	A549	lung:	n/a	chr19:41858550-41858559 chr19:41859909-41859918 chr19:41858546-41858559 chr19:41859459-41859472 chr19:41859906-41859924 chr19:41860035-41860053 chr19:41858544-41858562 chr19:41860037-41860050 chr19:41858547-41858557 chr19:41859906-41859919
2	POLR2A	chr19:41860926-41861330	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41855447..41861218-chr19:41901143..41905435,7	MCF-7	breast:
2	chr19:41847648..41852200-chr19:41855915..41861192,6	MCF-7	breast:
3	chr19:41770477..41773138-chr19:41858876..41861675,2	MCF-7	breast:
4	chr19:41825057..41828118-chr19:41860715..41862978,3	K562	blood:
5	chr19:41854267..41857215-chr19:41859856..41862250,3	MCF-7	breast:
6	chr19:41814082..41814803-chr19:41860791..41861367,2	K562	blood:
7	chr19:41858489..41863412-chr19:41867730..41871601,11	K562	blood:
8	chr19:41768247..41770079-chr19:41858302..41861510,3	MCF-7	breast:
9	chr19:41825498..41830119-chr19:41857290..41861615,7	MCF-7	breast:
10	chr19:41814729..41817632-chr19:41858391..41861046,3	K562	blood:
11	chr19:41855237..41861298-chr19:41901562..41905286,5	K562	blood:
12	chr19:41859512..41861303-chr19:41943975..41945825,3	K562	blood:
13	chr19:41825452..41832651-chr19:41855170..41863054,16	K562	blood:
14	chr19:41857565..41861683-chr19:41942530..41947234,4	MCF-7	breast:
15	chr19:41856910..41863042-chr19:41867113..41873191,18	MCF-7	breast:
16	chr19:41860169..41862147-chr19:41901440..41904683,3	MCF-7	breast:
17	chr19:41859535..41862336-chr19:41931235..41934067,2	MCF-7	breast:

Variant related genes	Relation type
TGFB1	TF binding region
ENSG00000248098	Chromatin interaction
ENSG00000268987	Chromatin interaction
ENSG00000268475	Chromatin interaction
ENSG00000077348	Chromatin interaction
ENSG00000123810	Chromatin interaction
ENSG00000105329	Chromatin interaction
ENSG00000105341	Chromatin interaction
ENSG00000142039	Chromatin interaction
ENSG00000142046	Chromatin interaction
ENSG00000177191	Chromatin interaction
ENSG00000255730	Chromatin interaction
ENSG00000105323	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs16975216	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1802868	chr19:41856886-41869392	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
2	nsv521311	chr19:41856886-41882712	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41858800-41861000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:41859600-41861000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr19:41859800-41861000	Enhancers	Liver	Liver
4	chr19:41859800-41862200	Enhancers	Primary B cells from cord blood	blood
5	chr19:41859800-41868200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr19:41860000-41863800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:41860200-41861000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:41860200-41862800	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr19:41860200-41864000	Weak transcription	Small Intestine	intestine
10	chr19:41860200-41864800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr19:41860200-41865000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:41860200-41869000	Weak transcription	Gastric	stomach
13	chr19:41860400-41861000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
14	chr19:41860400-41861000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
15	chr19:41860400-41861000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr19:41860400-41861000	Bivalent Enhancer	Fetal Stomach	stomach
17	chr19:41860400-41861400	Enhancers	Left Ventricle	heart
18	chr19:41860400-41862200	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr19:41860400-41862200	Enhancers	Placenta	Placenta
20	chr19:41860400-41862200	Enhancers	Right Atrium	heart
21	chr19:41860400-41862400	Enhancers	Lung	lung
22	chr19:41860400-41862600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:41860400-41862800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr19:41860400-41862800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr19:41860400-41862800	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr19:41860400-41862800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr19:41860400-41862800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr19:41860400-41863000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:41860400-41864400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr19:41860400-41864800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:41860400-41865800	Enhancers	Primary T cells fromperipheralblood	blood
32	chr19:41860400-41868200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr19:41860400-41868600	Weak transcription	GM12878-XiMat	blood
34	chr19:41860400-41868800	Weak transcription	Hela-S3	cervix
35	chr19:41860400-41869000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:41860400-41869000	Weak transcription	Brain Angular Gyrus	brain
37	chr19:41860400-41869000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr19:41860400-41869200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:41860400-41869200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr19:41860400-41869200	Weak transcription	HSMMtube	muscle
41	chr19:41860400-41869200	Weak transcription	HUVEC	blood vessel
42	chr19:41860400-41869200	Weak transcription	NHDF-Ad	bronchial
43	chr19:41860400-41869200	Weak transcription	NHLF	lung
44	chr19:41860400-41869400	Weak transcription	Aorta	Aorta
45	chr19:41860400-41869400	Weak transcription	Ovary	ovary
46	chr19:41860600-41861000	Bivalent Enhancer	Brain Germinal Matrix	brain
47	chr19:41860600-41861000	Genic enhancers	Fetal Brain Female	brain
48	chr19:41860600-41861000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
49	chr19:41860600-41861000	Enhancers	Dnd41	blood
50	chr19:41860600-41861000	Enhancers	HepG2	liver

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