Variant report

Variant	rs12459227
Chromosome Location	chr19:52641519-52641520
allele	A/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	MAZ	chr19:52641235-52643712	IMR90	lung:	n/a	chr19:52642119-52642130 chr19:52642119-52642130 chr19:52642120-52642129 chr19:52642115-52642134 chr19:52642120-52642130 chr19:52642119-52642130 chr19:52642120-52642129 chr19:52642120-52642129 chr19:52642120-52642130
2	MXI1	chr19:52641433-52644116	IMR90	lung:	n/a	chr19:52642119-52642128 chr19:52642121-52642130
3	MYC	chr19:52641371-52642652	MCF10A-Er-Src	breast:	n/a	chr19:52642119-52642130 chr19:52642119-52642130 chr19:52642120-52642129 chr19:52642115-52642134 chr19:52642120-52642130 chr19:52642119-52642130 chr19:52642120-52642129 chr19:52642120-52642129 chr19:52642120-52642130
4	SIN3A	chr19:52641454-52643653	H1-hESC	embryonic stem cell:	n/a	chr19:52642121-52642130 chr19:52642701-52642715
5	REST	chr19:52641344-52643566	H1-neurons	neurons:	n/a	chr19:52642591-52642604 chr19:52643241-52643254 chr19:52642700-52642714
6	MXI1	chr19:52641181-52643947	SK-N-SH	brain:	n/a	chr19:52642119-52642128 chr19:52642121-52642130

No.	Distal block	Cell Line	Cell type
1	chr19:52636537..52639802-chr19:52640245..52644732,7	K562	blood:
2	chr19:52636521..52639563-chr19:52639580..52641755,3	MCF-7	breast:
3	chr19:52641479..52644491-chr19:52690575..52695402,7	MCF-7	breast:
4	chr19:52641278..52644856-chr19:52672246..52674908,4	MCF-7	breast:
5	chr19:52641013..52643402-chr19:52771783..52774070,3	MCF-7	breast:
6	chr19:52641011..52643212-chr19:52671736..52674683,3	MCF-7	breast:
7	chr19:52641405..52644253-chr19:52691691..52696539,6	MCF-7	breast:

Variant related genes	Relation type
RPL37P23	TF binding region
ENSG00000268458	TF binding region
ENSG00000238630	TF binding region
ENSG00000105568	Chromatin interaction
ENSG00000267927	Chromatin interaction
ENSG00000196267	Chromatin interaction
ENSG00000267827	Chromatin interaction
ENSG00000196214	Chromatin interaction
ENSG00000238630	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11084145	0.92[JPT][hapmap]
rs12459201	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462872	0.92[JPT][hapmap]
rs16983496	0.85[JPT][hapmap]
rs17779542	0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs17835808	0.92[JPT][hapmap]
rs59541557	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60164622	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60937535	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61573127	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67170112	0.93[EUR][1000 genomes]
rs67602609	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67861844	0.93[EUR][1000 genomes]
rs8100114	0.85[JPT][hapmap]
rs8103346	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs8105609	0.85[JPT][hapmap]
rs8108125	0.85[JPT][hapmap]
rs8112502	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52616200-52641600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52629400-52641600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:52629600-52641800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:52633600-52641600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr19:52633800-52641600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr19:52634000-52642000	Weak transcription	Small Intestine	intestine
7	chr19:52634800-52641600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:52634800-52642000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:52636000-52641800	Weak transcription	Ovary	ovary
10	chr19:52637400-52641800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr19:52637600-52641800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr19:52639000-52641600	Weak transcription	Colonic Mucosa	Colon
13	chr19:52639000-52641800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:52639000-52642000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr19:52639200-52641600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr19:52640000-52642000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:52640200-52642000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:52640800-52641600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:52641000-52641600	Flanking Active TSS	Brain Germinal Matrix	brain
20	chr19:52641000-52641600	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr19:52641000-52641800	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr19:52641000-52643600	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr19:52641200-52641600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr19:52641200-52641600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr19:52641200-52641600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr19:52641200-52641600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:52641200-52641600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:52641200-52641600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:52641200-52641600	Enhancers	Liver	Liver
30	chr19:52641200-52641600	Enhancers	Esophagus	oesophagus
31	chr19:52641200-52641600	Transcr. at gene 5' and 3'	Fetal Brain Male	brain
32	chr19:52641200-52641600	Flanking Active TSS	Fetal Brain Female	brain
33	chr19:52641200-52641600	Enhancers	Fetal Intestine Small	intestine
34	chr19:52641200-52641600	Flanking Active TSS	Fetal Lung	lung
35	chr19:52641200-52641600	Enhancers	Fetal Muscle Trunk	muscle
36	chr19:52641200-52641600	Enhancers	Fetal Muscle Leg	muscle
37	chr19:52641200-52641600	Enhancers	Psoas Muscle	Psoas
38	chr19:52641200-52641600	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr19:52641200-52641600	Enhancers	Right Atrium	heart
40	chr19:52641200-52641600	Enhancers	Stomach Smooth Muscle	stomach
41	chr19:52641200-52641600	Enhancers	Spleen	Spleen
42	chr19:52641200-52641600	Flanking Active TSS	HMEC	breast
43	chr19:52641200-52641600	Flanking Active TSS	NHLF	lung
44	chr19:52641200-52641800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr19:52641200-52641800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr19:52641200-52641800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr19:52641200-52641800	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr19:52641200-52641800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:52641200-52641800	Enhancers	Brain Angular Gyrus	brain
50	chr19:52641200-52641800	Enhancers	Brain Cingulate Gyrus	brain

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