Variant report

Variant	rs2072350
Chromosome Location	chr19:38871182-38871183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:38870862-38871539	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:38870835-38871554	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:38870794-38872639	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:38869050-38873371	K562	blood:	n/a	n/a
5	POLR2A	chr19:38871004-38871381	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr19:38870838-38871373	HL-60	blood:	n/a	n/a
7	POLR2A	chr19:38869721-38871433	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr19:38870925-38871775	K562	blood:	n/a	n/a
9	POLR2A	chr19:38870768-38871942	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:38869603-38879135	K562	blood:	n/a	n/a
11	POLR2A	chr19:38870768-38871413	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr19:38870820-38871364	K562	blood:	n/a	n/a
13	POLR2A	chr19:38870886-38872073	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr19:38870902-38872103	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:38870771-38873361	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:38870783-38871275	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:38871099-38871432	HepG2	liver:	n/a	n/a
18	POLR2A	chr19:38870683-38871585	GM12892	blood:	n/a	n/a
19	POLR2A	chr19:38870991-38871247	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr19:38870862-38871212	GM12891	blood:	n/a	n/a
21	POLR2A	chr19:38870945-38871193	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:38870912-38871991	HepG2	liver:	n/a	n/a
23	POLR2A	chr19:38870875-38871563	GM12891	blood:	n/a	n/a
24	POLR2A	chr19:38870825-38871665	K562	blood:	n/a	n/a
25	POLR2A	chr19:38870877-38872941	A549	lung:	n/a	n/a
26	POLR2A	chr19:38870960-38871235	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:38833439..38835200-chr19:38870753..38873004,2	MCF-7	breast:
2	chr19:38824724..38826894-chr19:38868914..38871370,2	MCF-7	breast:
3	chr19:38799413..38800951-chr19:38868296..38871211,2	MCF-7	breast:
4	chr19:38753884..38755807-chr19:38870034..38871603,2	MCF-7	breast:

No data

Variant related genes	Relation type
PSMD8	TF binding region
ENSG00000267090	TF binding region
ENSG00000167642	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000167645	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1060455	1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11878707	1.00[GIH][hapmap]
rs12460181	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12460264	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12460599	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12461248	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12461700	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12462230	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12463175	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2074979	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2074980	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2074981	0.81[MEX][hapmap]
rs2286547	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2286550	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2286551	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302226	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35848839	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3745955	0.92[ASN][1000 genomes]
rs3745956	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3745960	0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3745961	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3745962	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3745964	0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4802399	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4802400	0.90[MEX][hapmap]
rs60577771	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60759642	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60915799	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61379500	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2072350	SPINT2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38866400-38876000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:38866800-38871600	Weak transcription	Small Intestine	intestine
3	chr19:38867000-38874600	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr19:38867000-38874800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:38867000-38874800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr19:38867000-38875600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr19:38867000-38877200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:38867000-38878000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr19:38867200-38871600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:38867200-38872000	Weak transcription	Stomach Mucosa	stomach
11	chr19:38867200-38874600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr19:38867200-38874800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:38867200-38874800	Strong transcription	Fetal Intestine Large	intestine
14	chr19:38867200-38875200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr19:38867200-38875400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:38867200-38877000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:38867200-38877200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr19:38867200-38877400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:38867400-38871800	Weak transcription	Fetal Brain Male	brain
20	chr19:38867400-38874400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr19:38867400-38875000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr19:38867400-38875800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr19:38867600-38872600	Weak transcription	Fetal Heart	heart
24	chr19:38867600-38872800	Strong transcription	NHEK	skin
25	chr19:38867600-38873000	Strong transcription	Placenta	Placenta
26	chr19:38867600-38873800	Strong transcription	Fetal Stomach	stomach
27	chr19:38867600-38874800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:38867600-38874800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr19:38867600-38875200	Strong transcription	Liver	Liver
30	chr19:38867600-38875400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:38867600-38875600	Strong transcription	Fetal Intestine Small	intestine
32	chr19:38867600-38875800	Strong transcription	Primary T cells from cord blood	blood
33	chr19:38867600-38876000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr19:38867600-38876200	Strong transcription	Brain Cingulate Gyrus	brain
35	chr19:38867600-38877400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:38867800-38871400	Weak transcription	Hela-S3	cervix
37	chr19:38867800-38871600	Strong transcription	Dnd41	blood
38	chr19:38867800-38871800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr19:38867800-38872200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:38867800-38873800	Strong transcription	Fetal Muscle Leg	muscle
41	chr19:38867800-38875000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr19:38867800-38875000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:38867800-38875200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:38867800-38875200	Strong transcription	Thymus	Thymus
45	chr19:38867800-38875400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr19:38867800-38875600	Strong transcription	Colon Smooth Muscle	Colon
47	chr19:38867800-38875800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr19:38867800-38875800	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr19:38867800-38876200	Strong transcription	Adipose Nuclei	Adipose
50	chr19:38867800-38876200	Strong transcription	Brain Hippocampus Middle	brain

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