Variant report

Variant	rs2232999
Chromosome Location	chr19:39111092-39111093
allele	C/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	chr19:39108616-39111427	K562	blood:	n/a	n/a
2	POLR2A	chr19:39107795-39111328	GM12878	blood:	n/a	n/a
3	SIN3AK20	chr19:39108443-39111312	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr19:39108158-39113791	PANC-1	pancreas:	n/a	n/a
5	CTCF	chr19:39110920-39111153	T-47D	breast:	n/a	n/a
6	POLR2A	chr19:39110996-39111291	HepG2	liver:	n/a	n/a
7	MAX	chr19:39108636-39111143	A549	lung:	n/a	chr19:39109723-39109732 chr19:39109604-39109614 chr19:39108656-39108666 chr19:39109718-39109737 chr19:39108653-39108663 chr19:39109721-39109734 chr19:39109723-39109732 chr19:39109721-39109729 chr19:39109721-39109734

No.	Distal block	Cell Line	Cell type
1	chr19:39106830..39111691-chr19:39117375..39123240,7	MCF-7	breast:
2	chr19:39086924..39089196-chr19:39110889..39112683,2	K562	blood:
3	chr19:39107241..39111219-chr19:39136508..39140596,7	K562	blood:
4	chr19:38986067..38987840-chr19:39110926..39112725,2	K562	blood:
5	chr19:39024830..39027065-chr19:39108421..39111246,2	MCF-7	breast:
6	chr19:39109264..39111637-chr19:39122200..39124366,4	MCF-7	breast:
7	chr19:39108167..39112213-chr19:39136508..39140596,7	K562	blood:
8	chr19:39110019..39112563-chr19:39114565..39116465,2	MCF-7	breast:

Variant related genes	Relation type
MAP4K1	TF binding region
ENSG00000178982	Chromatin interaction
ENSG00000267291	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000196218	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2232994	1.00[AMR][1000 genomes]
rs73552646	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	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
6	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39109800-39111200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
2	chr19:39110200-39111200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr19:39110200-39111200	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
4	chr19:39110200-39111200	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr19:39110400-39111200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:39110400-39111200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:39110400-39111200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr19:39110400-39111200	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
9	chr19:39110400-39111200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
10	chr19:39110400-39111200	Flanking Active TSS	Hela-S3	cervix
11	chr19:39110400-39111200	Transcr. at gene 5' and 3'	K562	blood
12	chr19:39110400-39111200	Flanking Active TSS	NHDF-Ad	bronchial
13	chr19:39110400-39122600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr19:39110600-39111200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:39110600-39111200	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
16	chr19:39110600-39111200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:39110600-39111200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr19:39110600-39111200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:39110600-39111200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:39110600-39111200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:39110600-39111200	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
22	chr19:39110600-39111200	Enhancers	Fetal Heart	heart
23	chr19:39110600-39111200	Genic enhancers	Placenta	Placenta
24	chr19:39110600-39111200	Enhancers	Placenta Amnion	Placenta Amnion
25	chr19:39110600-39111200	Flanking Active TSS	HepG2	liver
26	chr19:39110600-39112600	Weak transcription	Aorta	Aorta
27	chr19:39110800-39111200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:39110800-39111200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
29	chr19:39110800-39111200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
30	chr19:39110800-39111200	Genic enhancers	Primary B cells from peripheral blood	blood
31	chr19:39110800-39111200	Genic enhancers	Primary T cells from cord blood	blood
32	chr19:39110800-39111200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
33	chr19:39110800-39111200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr19:39110800-39111200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:39110800-39111200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr19:39110800-39111200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:39110800-39111200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:39110800-39111200	Genic enhancers	Liver	Liver
39	chr19:39110800-39111200	Transcr. at gene 5' and 3'	Brain Angular Gyrus	brain
40	chr19:39110800-39111200	Genic enhancers	Brain Inferior Temporal Lobe	brain
41	chr19:39110800-39111200	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
42	chr19:39110800-39111200	Genic enhancers	Fetal Brain Male	brain
43	chr19:39110800-39111200	Genic enhancers	Fetal Muscle Leg	muscle
44	chr19:39110800-39111200	Genic enhancers	Fetal Stomach	stomach
45	chr19:39110800-39111200	Genic enhancers	Fetal Thymus	thymus
46	chr19:39110800-39111200	Genic enhancers	Left Ventricle	heart
47	chr19:39110800-39111200	Genic enhancers	Lung	lung
48	chr19:39110800-39111200	Genic enhancers	Pancreas	Pancrea
49	chr19:39110800-39111200	Enhancers	Right Atrium	heart
50	chr19:39110800-39111200	Genic enhancers	Sigmoid Colon	Sigmoid Colon

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