Variant report

Variant	rs2302226
Chromosome Location	chr19:38866939-38866940
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:38866849-38867289	K562	blood:	n/a	n/a
2	POLR2A	chr19:38864742-38867713	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:38866778-38867647	K562	blood:	n/a	n/a
4	MXI1	chr19:38864586-38867349	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr19:38866939-38866942	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:38866826-38867156	GM12878	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38839437..38845026-chr19:38862738..38867726,6	MCF-7	breast:
2	chr19:38824024..38830842-chr19:38863522..38868048,10	MCF-7	breast:
3	chr19:38864536..38866994-chr19:38891927..38895682,4	MCF-7	breast:
4	chr19:38824766..38830853-chr19:38863348..38868089,16	MCF-7	breast:
5	chr19:38851019..38853857-chr19:38863435..38867110,13	MCF-7	breast:
6	chr19:38850348..38855103-chr19:38862504..38867180,11	K562	blood:
7	chr19:38753811..38757692-chr19:38863788..38867160,7	MCF-7	breast:
8	chr19:38849999..38854779-chr19:38863669..38868606,10	K562	blood:
9	chr19:38864731..38867116-chr19:38892888..38894994,2	MCF-7	breast:
10	chr19:38865264..38867147-chr19:38906342..38908608,2	MCF-7	breast:
11	chr19:38823410..38828693-chr19:38863569..38867873,9	K562	blood:
12	chr19:38865210..38867100-chr19:38887808..38889837,2	MCF-7	breast:
13	chr19:38825004..38828693-chr19:38863595..38867873,9	K562	blood:
14	chr19:38793026..38794538-chr19:38866336..38868984,2	K562	blood:
15	chr19:38865462..38867810-chr19:38887445..38890114,2	K562	blood:
16	chr19:38711690..38716111-chr19:38864242..38867673,4	MCF-7	breast:

No data

Variant related genes	Relation type
PSMD8	TF binding region
ENSG00000267473	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000011332	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000130244	Chromatin interaction
ENSG00000266963	Chromatin interaction
ENSG00000171777	Chromatin interaction
ENSG00000238838	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1060455	1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11878707	1.00[GIH][hapmap]
rs12460181	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12460264	0.89[ASN][1000 genomes]
rs12460599	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12461248	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12461700	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12462230	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12463175	0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2072350	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]
rs2074979	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2074980	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2074981	0.81[MEX][hapmap]
rs2286547	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2286550	0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286551	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35710536	1.00[ASW][hapmap]
rs35848839	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3745955	0.96[ASN][1000 genomes]
rs3745956	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3745960	0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3745961	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3745962	1.00[ASW][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3745964	1.00[JPT][hapmap]
rs4802399	1.00[JPT][hapmap]
rs4802400	0.90[MEX][hapmap]
rs60577771	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60759642	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60915799	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61379500	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[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
rs2302226	SPINT2	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38864600-38867000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr19:38864600-38867000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr19:38864600-38867000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr19:38865800-38867000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr19:38865800-38867200	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr19:38866000-38867000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr19:38866000-38867000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr19:38866000-38867000	Flanking Active TSS	Brain Anterior Caudate	brain
9	chr19:38866000-38867000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr19:38866000-38867000	Flanking Active TSS	Fetal Brain Female	brain
11	chr19:38866000-38867000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr19:38866000-38867000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr19:38866000-38867200	Flanking Active TSS	Right Ventricle	heart
14	chr19:38866000-38867600	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr19:38866200-38867000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr19:38866200-38867000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:38866200-38867000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr19:38866200-38867000	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr19:38866200-38867200	Flanking Active TSS	Hela-S3	cervix
20	chr19:38866200-38867200	Flanking Active TSS	Osteobl	bone
21	chr19:38866400-38867000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:38866400-38867000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:38866400-38867000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr19:38866400-38867000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr19:38866400-38867000	Weak transcription	Aorta	Aorta
26	chr19:38866400-38867000	Enhancers	Lung	lung
27	chr19:38866400-38867000	Enhancers	Ovary	ovary
28	chr19:38866400-38867000	Flanking Active TSS	HMEC	breast
29	chr19:38866400-38867200	Enhancers	Primary B cells from peripheral blood	blood
30	chr19:38866400-38867200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr19:38866400-38867200	Enhancers	Esophagus	oesophagus
32	chr19:38866400-38867200	Enhancers	Stomach Mucosa	stomach
33	chr19:38866400-38867200	Transcr. at gene 5' and 3'	K562	blood
34	chr19:38866400-38867400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
35	chr19:38866400-38867600	Enhancers	Fetal Heart	heart
36	chr19:38866400-38867600	Transcr. at gene 5' and 3'	NHEK	skin
37	chr19:38866400-38869800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:38866400-38870000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:38866400-38876000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr19:38866600-38867000	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr19:38866600-38867000	Flanking Active TSS	NHDF-Ad	bronchial
42	chr19:38866600-38867200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:38866600-38867200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:38866600-38867200	Genic enhancers	Fetal Intestine Large	intestine
45	chr19:38866600-38867200	Enhancers	Pancreas	Pancrea
46	chr19:38866600-38867200	Enhancers	Placenta Amnion	Placenta Amnion
47	chr19:38866600-38867200	Transcr. at gene 5' and 3'	A549	lung
48	chr19:38866600-38867600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
49	chr19:38866600-38867600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr19:38866600-38867600	Genic enhancers	Cortex derived primary cultured neurospheres	brain

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