Variant report

Variant	rs2239948
Chromosome Location	chr19:36247507-36247508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:36247429-36249863	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr19:36243424-36249712	IMR90	lung:	n/a	n/a
3	POLR2A	chr19:36247499-36249815	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr19:36247442-36249646	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr19:36247073-36249660	U87	brain:	n/a	n/a
6	MAZ	chr19:36245970-36249729	IMR90	lung:	n/a	chr19:36246654-36246663
7	POLR2A	chr19:36247497-36249596	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr19:36246821-36249566	K562	blood:	n/a	n/a
9	POLR2A	chr19:36247425-36247517	K562	blood:	n/a	n/a
10	POLR2A	chr19:36247499-36249516	U87	brain:	n/a	n/a
11	POLR2A	chr19:36247448-36249539	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr19:36246847-36249576	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:36246837-36249942	PANC-1	pancreas:	n/a	n/a
14	MXI1	chr19:36246145-36247840	IMR90	lung:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:36247404..36252021-chr19:36265348..36272678,7	MCF-7	breast:
2	chr19:36206099..36210841-chr19:36246614..36251827,8	MCF-7	breast:
3	chr19:36245255..36250047-chr19:36263979..36267864,8	K562	blood:
4	chr19:36238866..36244880-chr19:36246037..36252437,21	MCF-7	breast:

No data

Variant related genes	Relation type
C19orf55	TF binding region
ENSG00000267439	TF binding region
ENSG00000004777	Chromatin interaction
ENSG00000272333	Chromatin interaction
ENSG00000267439	Chromatin interaction
ENSG00000267796	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2234363	0.93[ASN][1000 genomes]
rs2242524	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2267587	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs34885866	1.00[AFR][1000 genomes]
rs35443549	0.81[ASN][1000 genomes]
rs3746276	0.96[ASN][1000 genomes]
rs3746279	0.96[ASN][1000 genomes]
rs3761090	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap]
rs3761091	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs3787052	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3810453	0.88[ASN][1000 genomes]
rs4145402	0.96[ASN][1000 genomes]
rs55703687	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv911635	chr19:36217333-36283847	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv458567	chr19:36221051-36283847	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
14	nsv579423	chr19:36221051-36283847	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
15	nsv911636	chr19:36240960-36290977	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2239948	LIN37	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36241000-36247600	Weak transcription	HMEC	breast
2	chr19:36241200-36247800	Weak transcription	Hela-S3	cervix
3	chr19:36243800-36247800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
4	chr19:36244600-36247600	Weak transcription	GM12878-XiMat	blood
5	chr19:36245200-36247800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:36245400-36247600	Weak transcription	Dnd41	blood
7	chr19:36245600-36247600	Weak transcription	Brain Angular Gyrus	brain
8	chr19:36245600-36247800	Weak transcription	Brain Substantia Nigra	brain
9	chr19:36245600-36247800	Weak transcription	HepG2	liver
10	chr19:36245600-36248000	Weak transcription	K562	blood
11	chr19:36245800-36247600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr19:36245800-36248400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:36246000-36248000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
14	chr19:36246000-36248000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr19:36246000-36248200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
16	chr19:36246000-36248400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr19:36246000-36248600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:36246000-36248600	Enhancers	Spleen	Spleen
19	chr19:36246000-36248800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:36246000-36248800	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr19:36246000-36248800	Flanking Active TSS	Fetal Muscle Trunk	muscle
22	chr19:36246000-36249800	Active TSS	H9 Cell Line	embryonic stem cell
23	chr19:36246200-36247600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr19:36246200-36247600	Enhancers	HUVEC	blood vessel
25	chr19:36246200-36247800	Enhancers	Primary T cells from cord blood	blood
26	chr19:36246200-36248200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:36246200-36248400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:36246200-36248400	Flanking Active TSS	Left Ventricle	heart
29	chr19:36246200-36248600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr19:36246200-36248600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr19:36246200-36248800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr19:36246200-36248800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:36246200-36249400	Active TSS	Aorta	Aorta
34	chr19:36246200-36250000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:36246400-36247600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:36246400-36247600	Active TSS	Stomach Smooth Muscle	stomach
37	chr19:36246400-36247600	Active TSS	Osteobl	bone
38	chr19:36246400-36247800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
39	chr19:36246400-36247800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:36246400-36247800	Active TSS	Colon Smooth Muscle	Colon
41	chr19:36246400-36248000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
42	chr19:36246400-36248000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
43	chr19:36246400-36248000	Enhancers	HSMMtube	muscle
44	chr19:36246400-36248800	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr19:36246400-36249800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr19:36246400-36249800	Active TSS	Rectal Smooth Muscle	rectum
47	chr19:36246400-36250000	Active TSS	Psoas Muscle	Psoas
48	chr19:36246400-36250200	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr19:36246600-36247600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:36246600-36247600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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