Variant report

Variant	rs1000245
Chromosome Location	chr19:19031087-19031088
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr19:19029389-19031297	MCF-7	breast:	n/a	chr19:19030008-19030017
2	CREB1	chr19:19029478-19031091	GM12878	blood:	n/a	chr19:19030474-19030487
3	POLR2A	chr19:19029226-19031741	HL-60	blood:	n/a	n/a
4	POLR2A	chr19:19029579-19031581	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr19:19029557-19031368	MCF10A-Er-Src	breast:	n/a	n/a
6	MXI1	chr19:19029306-19031732	IMR90	lung:	n/a	n/a
7	POLR2A	chr19:19029076-19031291	IMR90	lung:	n/a	n/a
8	POLR2A	chr19:19029254-19031502	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr19:19031065-19031133	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr19:19031006-19031576	HepG2	liver:	n/a	n/a
11	HCFC1	chr19:19029224-19031350	Hela-S3	cervix:	n/a	n/a
12	SP1	chr19:19029688-19031097	HCT-116	colon:	n/a	chr19:19029991-19030003 chr19:19029993-19030002 chr19:19029992-19030006 chr19:19030292-19030306 chr19:19030448-19030469 chr19:19030295-19030306 chr19:19030355-19030376 chr19:19029991-19030003
13	POLR2A	chr19:19029324-19031660	HL-60	blood:	n/a	n/a
14	MXI1	chr19:19029020-19031590	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr19:19029461-19031532	U87	brain:	n/a	n/a
16	POLR2A	chr19:19029467-19031488	U87	brain:	n/a	n/a
17	POLR2A	chr19:19031049-19031582	U87	brain:	n/a	n/a
18	BHLHE40	chr19:19030921-19031238	K562	blood:	n/a	n/a
19	WRNIP1	chr19:19029512-19031387	GM12878	blood:	n/a	n/a
20	TEAD4	chr19:19029443-19031096	K562	blood:	n/a	n/a
21	SMC3	chr19:19031051-19031088	HepG2	liver:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19014514..19025012-chr19:19028545..19031608,12	MCF-7	breast:
2	chr17:62221757..62224608-chr19:19030239..19032078,2	MCF-7	breast:
3	chr19:19028307..19038067-chr19:19048419..19054729,15	MCF-7	breast:
4	chr19:19028142..19040542-chr19:19046967..19057144,34	MCF-7	breast:
5	chr19:18699463..18701468-chr19:19028694..19031158,3	K562	blood:
6	chr19:19005129..19007826-chr19:19028734..19032982,4	MCF-7	breast:
7	chr19:18555810..18558424-chr19:19028708..19031515,2	K562	blood:
8	chr19:18942543..18946544-chr19:19028586..19032596,4	MCF-7	breast:
9	chr19:19028947..19031173-chr19:19514626..19517474,2	K562	blood:
10	chr19:19005501..19008972-chr19:19028688..19032169,4	K562	blood:
11	chr19:18699463..18701468-chr19:19028694..19031158,2	K562	blood:
12	chr19:19010579..19012422-chr19:19029682..19031277,2	K562	blood:
13	chr17:58602348..58605057-chr19:19030634..19032136,2	MCF-7	breast:
14	chr19:19023442..19028090-chr19:19028276..19032184,6	MCF-7	breast:
15	chr19:19028699..19031698-chr19:19049211..19052149,3	K562	blood:

No data

Variant related genes	Relation type
DDX49	TF binding region
COPE	TF binding region
ENSG00000130283	Chromatin interaction
ENSG00000167491	Chromatin interaction
ENSG00000105656	Chromatin interaction
ENSG00000266402	Chromatin interaction
ENSG00000259349	Chromatin interaction
ENSG00000005007	Chromatin interaction
ENSG00000105669	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000223802	Chromatin interaction
ENSG00000062725	Chromatin interaction
ENSG00000269019	Chromatin interaction
ENSG00000199753	Chromatin interaction
ENSG00000051128	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1000244	1.00[YRI][hapmap]
rs16995755	1.00[AMR][1000 genomes]
rs16995781	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7255787	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911293	chr19:18872917-19050957	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv911294	chr19:18872917-19093619	Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv911297	chr19:18928480-19077385	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv911298	chr19:18928480-19093619	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911300	chr19:18944025-19093619	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv470132	chr19:18964442-19054720	Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv911301	chr19:18994638-19077385	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
8	nsv911302	chr19:18995201-19088981	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
10	nsv543926	chr19:19029529-19062771	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19028600-19031400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr19:19028800-19031200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:19028800-19031200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:19028800-19031200	Active TSS	GM12878-XiMat	blood
5	chr19:19028800-19031200	Active TSS	K562	blood
6	chr19:19029000-19031200	Active TSS	Right Atrium	heart
7	chr19:19029000-19031200	Active TSS	HSMM	muscle
8	chr19:19029000-19031200	Active TSS	NHDF-Ad	bronchial
9	chr19:19029000-19031200	Active TSS	NHLF	lung
10	chr19:19029000-19031400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr19:19029000-19031600	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr19:19029200-19031200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr19:19029200-19031200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr19:19029200-19031200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr19:19029200-19031200	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr19:19029200-19031200	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr19:19029200-19031200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:19029200-19031200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:19029200-19031200	Active TSS	Muscle Satellite Cultured Cells	--
20	chr19:19029200-19031200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:19029200-19031200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:19029200-19031200	Active TSS	Fetal Kidney	kidney
23	chr19:19029200-19031200	Active TSS	Ovary	ovary
24	chr19:19029200-19031200	Active TSS	Pancreas	Pancrea
25	chr19:19029200-19031200	Active TSS	Psoas Muscle	Psoas
26	chr19:19029200-19031200	Active TSS	HSMMtube	muscle
27	chr19:19029200-19031600	Active TSS	A549	lung
28	chr19:19029400-19031200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:19029400-19031200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr19:19029400-19031200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:19029400-19031200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:19029400-19031200	Active TSS	Placenta Amnion	Placenta Amnion
33	chr19:19029400-19031200	Bivalent/Poised TSS	HepG2	liver
34	chr19:19029400-19031600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:19029600-19031200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:19029600-19031200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:19029600-19031200	Active TSS	Fetal Intestine Small	intestine
38	chr19:19029600-19031200	Active TSS	Lung	lung
39	chr19:19030600-19031200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:19030600-19031200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:19030600-19031200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:19030600-19031400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr19:19030600-19031400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr19:19030600-19031400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr19:19030600-19031400	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr19:19030600-19031600	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr19:19030600-19031600	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr19:19030600-19031600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr19:19030600-19031600	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr19:19030600-19031600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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