Variant report

Variant	rs880090
Chromosome Location	chr19:19740729-19740730
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:74)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:74 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:19740600-19740750	AG04450	lung:	n/a	n/a
2	CTCF	chr19:19740660-19740810	HA-sp	spinal cord:	n/a	n/a
3	CTCF	chr19:19740620-19740770	HPF	lung:	n/a	n/a
4	POLR2A	chr19:19740187-19742607	GM12892	blood:	n/a	n/a
5	CTCF	chr19:19740640-19740790	HPAF	blood vessel:	n/a	n/a
6	CTCF	chr19:19740640-19740790	GM06990	blood:	n/a	n/a
7	CTCF	chr19:19740600-19740750	AG09319	gingival:	n/a	n/a
8	CTCF	chr19:19740580-19740730	GM12872	blood:	n/a	n/a
9	CTCF	chr19:19740580-19740730	NHDF-neo	bronchial:	n/a	n/a
10	CTCF	chr19:19740580-19740730	HEK293	kidney:	n/a	n/a
11	CTCF	chr19:19740620-19740770	HepG2	liver:	n/a	n/a
12	CTCF	chr19:19740680-19740830	HCM	heart:	n/a	n/a
13	CTCF	chr19:19740600-19740750	HPAF	blood vessel:	n/a	n/a
14	CTCF	chr19:19740670-19740749	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr19:19740660-19740810	AG10803	skin:	n/a	n/a
16	CTCF	chr19:19740580-19740730	AG04449	skin:	n/a	n/a
17	CTCF	chr19:19740620-19740770	HRE	kidney:	n/a	n/a
18	CTCF	chr19:19740580-19740730	HCFaa	heart:	n/a	n/a
19	CTCF	chr19:19740640-19740790	GM12875	blood:	n/a	n/a
20	CTCF	chr19:19740620-19740770	BJ	skin:	n/a	n/a
21	CTCF	chr19:19740580-19740730	MCF-7	breast:	n/a	n/a
22	POLR2A	chr19:19740291-19740750	GM12891	blood:	n/a	n/a
23	CTCF	chr19:19740680-19740830	AoAF	blood vessel:	n/a	n/a
24	CTCF	chr19:19740640-19740790	GM12872	blood:	n/a	n/a
25	CTCF	chr19:19740640-19740790	HMEC	breast:	n/a	n/a
26	CTCF	chr19:19740600-19740750	SK-N-SH_RA	brain:	n/a	n/a
27	CTCF	chr19:19740600-19740750	GM12866	blood:	n/a	n/a
28	POLR2A	chr19:19740639-19741218	GM12878	blood:	n/a	n/a
29	CTCF	chr19:19740720-19740870	HFF	foreskin:	n/a	n/a
30	CTCF	chr19:19740700-19740850	GM12873	blood:	n/a	n/a
31	CTCF	chr19:19740600-19740750	A549	lung:	n/a	n/a
32	CTCF	chr19:19740580-19740730	HMF	breast:	n/a	n/a
33	CTCF	chr19:19740660-19740810	SAEC	small airway:	n/a	n/a
34	CTCF	chr19:19740580-19740730	SAEC	small airway:	n/a	n/a
35	CTCF	chr19:19740600-19740750	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr19:19740127-19740745	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr19:19740538-19740734	GM12891	blood:	n/a	n/a
38	CTCF	chr19:19740620-19740770	MCF-7	breast:	n/a	n/a
39	CTCF	chr19:19740580-19740730	HCT-116	colon:	n/a	n/a
40	CTCF	chr19:19740700-19740850	GM12869	blood:	n/a	n/a
41	CTCF	chr19:19740620-19740770	HEEpiC	esophagus:	n/a	n/a
42	POLR2A	chr19:19740697-19741208	GM12878	blood:	n/a	n/a
43	CTCF	chr19:19740660-19740810	HRE	kidney:	n/a	n/a
44	POLR2A	chr19:19740105-19742556	GM12878	blood:	n/a	n/a
45	CTCF	chr19:19740620-19740770	HCPEpiC	choroid plexus:	n/a	n/a
46	POLR2A	chr19:19740161-19741847	GM12891	blood:	n/a	n/a
47	CTCF	chr19:19740600-19740750	HA-sp	spinal cord:	n/a	n/a
48	CTCF	chr19:19740580-19740730	HUVEC	blood vessel:	n/a	n/a
49	CTCF	chr19:19740660-19740810	HBMEC	blood vessel:	n/a	n/a
50	CTCF	chr19:19740640-19740790	Hela-S3	cervix:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19739216..19741548-chr19:19773041..19775101,2	K562	blood:
2	chr19:19649974..19652165-chr19:19739340..19740963,2	MCF-7	breast:
3	chr19:19699149..19708161-chr19:19735507..19742255,11	MCF-7	breast:
4	chr19:19738621..19740217-chr19:19740622..19743235,2	MCF-7	breast:
5	chr19:19689040..19691188-chr19:19737339..19740827,3	MCF-7	breast:
6	chr19:19641380..19649124-chr19:19737025..19742358,12	MCF-7	breast:
7	chr19:19736821..19742043-chr19:19751528..19755876,8	MCF-7	breast:
8	chr19:19650041..19652184-chr19:19740271..19743058,2	K562	blood:
9	chr19:19737308..19740984-chr19:19746364..19748680,3	MCF-7	breast:
10	chr19:19740689..19742401-chr19:19765129..19766900,2	MCF-7	breast:

No data

Variant related genes	Relation type
LPAR2	TF binding region
ENSG00000105726	Chromatin interaction
ENSG00000105717	Chromatin interaction
ENSG00000267178	Chromatin interaction
ENSG00000160161	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000089639	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10403759	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10407283	0.96[YRI][hapmap]
rs10416924	0.83[YRI][hapmap]
rs11878202	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11879838	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12976826	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16994684	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16996174	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1968047	0.92[ASN][1000 genomes]
rs2043293	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2304129	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs34725331	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808974	0.96[ASN][1000 genomes]
rs6511040	0.83[YRI][hapmap]
rs6511046	0.86[YRI][hapmap]
rs7248200	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs7252228	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs739461	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8101679	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8113682	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs873870	0.93[YRI][hapmap];0.82[AFR][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	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs880090	DDX49	cis	cerebellum	SCAN
rs880090	SUGP2	cis	parietal	SCAN
rs880090	UNC13A	cis	cerebellum	SCAN
rs880090	OR10H4	cis	parietal	SCAN
rs880090	EDG4	cis	multi-tissue	Pritchard
rs880090	GATAD2A	cis	parietal	SCAN
rs880090	MED26	cis	parietal	SCAN
rs880090	IL12RB1	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19729800-19744400	Weak transcription	HSMMtube	muscle
2	chr19:19735000-19753200	Weak transcription	K562	blood
3	chr19:19738600-19744200	Weak transcription	Liver	Liver
4	chr19:19738600-19753000	Weak transcription	Fetal Brain Male	brain
5	chr19:19738800-19743400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:19738800-19752800	Weak transcription	Stomach Mucosa	stomach
7	chr19:19739000-19743400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr19:19739000-19744000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr19:19739000-19744400	Weak transcription	NHDF-Ad	bronchial
10	chr19:19739000-19745000	Weak transcription	HSMM	muscle
11	chr19:19739200-19742000	Weak transcription	Aorta	Aorta
12	chr19:19739400-19741000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:19739600-19744400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr19:19739800-19740800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr19:19739800-19741400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr19:19739800-19742000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr19:19739800-19742000	Weak transcription	NHEK	skin
18	chr19:19739800-19743200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr19:19739800-19743400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:19739800-19743400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:19739800-19743400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr19:19739800-19743600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr19:19739800-19744000	Weak transcription	Osteobl	bone
24	chr19:19739800-19744200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr19:19739800-19744200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr19:19739800-19744400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:19739800-19744600	Weak transcription	Brain Hippocampus Middle	brain
28	chr19:19739800-19744800	Weak transcription	Esophagus	oesophagus
29	chr19:19739800-19744800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr19:19739800-19745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:19739800-19745200	Weak transcription	Right Ventricle	heart
32	chr19:19739800-19745600	Weak transcription	Ovary	ovary
33	chr19:19739800-19752600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:19739800-19753200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:19739800-19753400	Weak transcription	Small Intestine	intestine
36	chr19:19739800-19753400	Weak transcription	HMEC	breast
37	chr19:19739800-19753600	Weak transcription	Brain Angular Gyrus	brain
38	chr19:19739800-19753600	Weak transcription	Brain Substantia Nigra	brain
39	chr19:19739800-19753600	Weak transcription	Left Ventricle	heart
40	chr19:19739800-19753600	Weak transcription	Right Atrium	heart
41	chr19:19740000-19740800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr19:19740000-19740800	Weak transcription	Fetal Stomach	stomach
43	chr19:19740000-19740800	Genic enhancers	Monocytes-CD14+_RO01746	blood
44	chr19:19740000-19741000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr19:19740000-19741000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:19740000-19741000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:19740000-19741000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:19740000-19741200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr19:19740000-19741600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:19740000-19741600	Weak transcription	Duodenum Mucosa	Duodenum

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