Variant report

Variant	rs2288528
Chromosome Location	chr19:55667500-55667501
allele	A/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	SIN3A	chr19:55667439-55668479	H1-hESC	embryonic stem cell:	n/a	n/a
2	MXI1	chr19:55667358-55667705	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:55667406-55669499	K562	blood:	n/a	n/a
4	YY1	chr19:55667359-55667620	SK-N-SH_RA	brain:	n/a	n/a
5	GABPA	chr19:55667465-55668164	K562	blood:	n/a	chr19:55667871-55667880
6	NR2F2	chr19:55667449-55668379	K562	blood:	n/a	n/a
7	YY1	chr19:55667269-55667568	SK-N-SH_RA	brain:	n/a	n/a
8	SP1	chr19:55667311-55668566	H1-hESC	embryonic stem cell:	n/a	chr19:55667850-55667860 chr19:55667918-55667930 chr19:55668322-55668331 chr19:55668344-55668356 chr19:55667869-55667881 chr19:55668153-55668165 chr19:55667919-55667933 chr19:55668321-55668333 chr19:55667870-55667880 chr19:55668322-55668331 chr19:55668154-55668164 chr19:55668344-55668356 chr19:55667918-55667929 chr19:55667920-55667929 chr19:55667870-55667880 chr19:55667919-55667928 chr19:55668153-55668165 chr19:55667869-55667881 chr19:55667870-55667879 chr19:55667901-55667912 chr19:55667870-55667879 chr19:55667918-55667930 chr19:55668321-55668333 chr19:55668323-55668332 chr19:55667871-55667880 chr19:55668154-55668164 chr19:55667870-55667884 chr19:55668322-55668336
9	MAX	chr19:55667282-55668377	K562	blood:	n/a	chr19:55668118-55668127
10	HMGN3	chr19:55667447-55668140	K562	blood:	n/a	n/a
11	MAX	chr19:55667293-55668316	H1-hESC	embryonic stem cell:	n/a	chr19:55668118-55668127
12	POLR2A	chr19:55667494-55668614	SK-N-MC	brain:	n/a	n/a
13	ZBTB7A	chr19:55667485-55670788	K562	blood:	n/a	n/a
14	YY1	chr19:55667364-55667760	A549	lung:	n/a	n/a
15	MAX	chr19:55667294-55668245	A549	lung:	n/a	chr19:55668118-55668127
16	YY1	chr19:55667300-55667851	K562	blood:	n/a	n/a
17	YY1	chr19:55667239-55667754	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55667256..55669360-chr19:55970897..55972567,2	K562	blood:
2	chr19:55666494..55670422-chr19:55672733..55675574,3	K562	blood:
3	chr19:55658387..55665037-chr19:55666866..55670836,8	K562	blood:
4	chr19:55627863..55630542-chr19:55666165..55668037,2	K562	blood:
5	chr19:55666595..55669878-chr19:55917801..55921094,4	K562	blood:
6	chr19:55627602..55630542-chr19:55666165..55668443,2	K562	blood:
7	chr19:55655324..55657835-chr19:55666870..55669444,2	K562	blood:
8	chr19:55666873..55668722-chr19:55676430..55678695,2	K562	blood:
9	chr19:55627370..55629030-chr19:55666382..55669249,2	MCF-7	breast:

Variant related genes	Relation type
TNNI3	TF binding region
ENSG00000267577	TF binding region
ENSG00000063241	Chromatin interaction
ENSG00000105048	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000239137	Chromatin interaction
ENSG00000167646	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10421953	0.82[ASN][1000 genomes]
rs10423713	0.83[ASN][1000 genomes]
rs1128712	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12459688	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12459887	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12459917	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12459921	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12459930	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12460445	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12461148	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12461170	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12461195	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12461202	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12462211	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17458	0.82[AMR][1000 genomes]
rs2071572	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2071574	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288420	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs2288518	1.00[CEU][hapmap]
rs2288529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301278	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[AMR][1000 genomes]
rs3745922	0.82[AMR][1000 genomes]
rs3786867	1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs3826887	0.84[AMR][1000 genomes]
rs3848618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3859544	0.89[ASN][1000 genomes]
rs56666700	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56726774	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58017412	0.82[AMR][1000 genomes]
rs58218194	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58824375	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59663064	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60176657	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60799292	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61570139	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7248997	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7255625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs890871	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9710458	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2485681	chr19:55665907-55667579	Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55666400-55669400	Active TSS	Left Ventricle	heart
2	chr19:55667000-55667600	Weak transcription	Fetal Heart	heart
3	chr19:55667200-55667600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr19:55667200-55667800	Bivalent/Poised TSS	Fetal Brain Female	brain
5	chr19:55667200-55668000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:55667200-55668400	Active TSS	H1 Cell Line	embryonic stem cell
7	chr19:55667200-55668400	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr19:55667200-55668400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:55667200-55668600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
10	chr19:55667200-55668600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
11	chr19:55667200-55668800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr19:55667200-55669200	Active TSS	Right Atrium	heart
13	chr19:55667400-55667600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:55667400-55667600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:55667400-55667600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:55667400-55667600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:55667400-55667600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
18	chr19:55667400-55667600	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr19:55667400-55667600	Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr19:55667400-55667600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
21	chr19:55667400-55667600	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
22	chr19:55667400-55667600	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
23	chr19:55667400-55667600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:55667400-55667600	Bivalent Enhancer	Colonic Mucosa	Colon
25	chr19:55667400-55667600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
26	chr19:55667400-55667600	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
27	chr19:55667400-55667600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
28	chr19:55667400-55667600	Flanking Active TSS	Fetal Kidney	kidney
29	chr19:55667400-55667600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
30	chr19:55667400-55667600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
31	chr19:55667400-55667600	Active TSS	HMEC	breast
32	chr19:55667400-55667600	Flanking Active TSS	K562	blood
33	chr19:55667400-55667600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
34	chr19:55667400-55667600	Flanking Bivalent TSS/Enh	NHEK	skin
35	chr19:55667400-55667600	Bivalent/Poised TSS	NHLF	lung
36	chr19:55667400-55667800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:55667400-55667800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:55667400-55667800	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
39	chr19:55667400-55667800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:55667400-55667800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:55667400-55667800	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:55667400-55667800	Bivalent Enhancer	Brain Angular Gyrus	brain
43	chr19:55667400-55667800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
44	chr19:55667400-55667800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
45	chr19:55667400-55667800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
46	chr19:55667400-55667800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
47	chr19:55667400-55667800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
48	chr19:55667400-55667800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
49	chr19:55667400-55667800	Enhancers	Ovary	ovary
50	chr19:55667400-55667800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum

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