Variant report

Variant	rs2363643
Chromosome Location	chr14:77788908-77788909
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr14:77788897-77788964	GM19238	blood:	n/a	n/a
2	POLR2A	chr14:77786461-77788955	GM12891	blood:	n/a	n/a
3	CTCF	chr14:77788901-77788945	GM12878	blood:	n/a	n/a
4	CTCF	chr14:77788800-77788950	Caco-2	colon:	n/a	n/a
5	USF2	chr14:77788861-77789137	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr14:77788897-77788945	MCF-7	breast:	n/a	n/a
7	CTCF	chr14:77788854-77788971	MCF-7	breast:	n/a	n/a
8	POLR2A	chr14:77786184-77789280	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr14:77788873-77788958	MCF-7	breast:	n/a	n/a
10	RAD21	chr14:77788865-77788977	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr14:77788820-77788970	MCF-7	breast:	n/a	n/a
12	SRF	chr14:77788650-77789377	MCF-7	breast:	n/a	chr14:77788965-77788976 chr14:77788962-77788976 chr14:77788961-77788975 chr14:77788966-77788975 chr14:77788964-77788977 chr14:77788964-77788977 chr14:77788966-77788980 chr14:77788962-77788980
13	POLR2A	chr14:77786459-77789015	SK-N-MC	brain:	n/a	n/a
14	CTCF	chr14:77788843-77788970	MCF-7	breast:	n/a	n/a
15	POLR2A	chr14:77788644-77789064	MCF-7	breast:	n/a	n/a
16	CTCF	chr14:77788800-77788950	GM12878	blood:	n/a	n/a
17	CTCF	chr14:77788800-77788950	HMF	breast:	n/a	n/a
18	CTCF	chr14:77788780-77788930	WERI-Rb-1	eye:	n/a	n/a
19	CTCF	chr14:77788780-77788930	HMEC	breast:	n/a	n/a
20	CTCF	chr14:77788820-77788970	GM12866	blood:	n/a	n/a
21	POLR2A	chr14:77788677-77789408	HepG2	liver:	n/a	n/a
22	MXI1	chr14:77786287-77789094	SK-N-SH	brain:	n/a	chr14:77786739-77786754
23	CTCF	chr14:77788900-77789050	A549	lung:	n/a	n/a
24	CTCF	chr14:77788880-77789030	GM12871	blood:	n/a	n/a
25	MXI1	chr14:77786162-77788939	IMR90	lung:	n/a	chr14:77786739-77786754
26	CTCF	chr14:77788900-77789050	GM12873	blood:	n/a	n/a
27	CTCF	chr14:77788800-77788950	HBMEC	blood vessel:	n/a	n/a
28	CTCF	chr14:77788860-77789010	HepG2	liver:	n/a	n/a
29	POLR2A	chr14:77786495-77789217	PBDE	blood:	n/a	n/a
30	CTCF	chr14:77788831-77789071	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr14:77639702..77642054-chr14:77787547..77789346,2	MCF-7	breast:
2	chr14:77787369..77789536-chr14:77923983..77928279,4	K562	blood:
3	chr14:77787549..77790264-chr14:77928506..77931057,2	MCF-7	breast:
4	chr14:77785598..77789538-chr14:77924091..77927637,5	MCF-7	breast:
5	chr14:77605681..77608147-chr14:77785721..77788952,4	MCF-7	breast:
6	chr14:77646577..77649681-chr14:77786771..77790034,4	MCF-7	breast:
7	chr14:77786062..77789367-chr14:77922502..77925939,5	K562	blood:
8	chr14:77355116..77357952-chr14:77787367..77789205,2	MCF-7	breast:
9	chr14:77559718..77567556-chr14:77781210..77790475,16	MCF-7	breast:
10	chr14:77785522..77790160-chr14:77881086..77890187,11	MCF-7	breast:
11	chr14:77604510..77610221-chr14:77785583..77789070,6	MCF-7	breast:
12	chr14:77785710..77794377-chr14:77836948..77846491,26	MCF-7	breast:
13	chr14:77786728..77789222-chr14:77922439..77925921,5	MCF-7	breast:
14	chr14:77788050..77790932-chr19:12894264..12897215,2	MCF-7	breast:
15	chr14:77786039..77790135-chr14:77842733..77846742,6	MCF-7	breast:

No data

Variant related genes	Relation type
GSTZ1	TF binding region
POMT2	TF binding region
ENSG00000100591	Chromatin interaction
ENSG00000258552	Chromatin interaction
ENSG00000100583	Chromatin interaction
ENSG00000177108	Chromatin interaction
ENSG00000269883	Chromatin interaction
ENSG00000267212	Chromatin interaction
ENSG00000259164	Chromatin interaction
ENSG00000198894	Chromatin interaction
ENSG00000151445	Chromatin interaction
ENSG00000165555	Chromatin interaction
ENSG00000100580	Chromatin interaction
ENSG00000268156	Chromatin interaction
ENSG00000223174	Chromatin interaction
ENSG00000165548	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11624564	0.82[CHB][hapmap]
rs11624859	0.82[ASN][1000 genomes]
rs11627257	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs17105672	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs2042045	0.83[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2111699	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2193594	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2216089	0.82[CHB][hapmap]
rs2270421	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2270423	0.83[ASW][hapmap];0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap]
rs2287387	0.91[CHB][hapmap]
rs2287395	0.92[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.80[EUR][1000 genomes]
rs2363641	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2363642	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2885854	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759733	0.93[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs3815626	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4147578	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4147579	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4899650	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs4903567	0.91[CHB][hapmap]
rs4903569	0.85[ASN][1000 genomes]
rs59630055	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61990299	0.82[ASN][1000 genomes]
rs6574367	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6574368	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67873774	0.82[ASN][1000 genomes]
rs7142812	0.86[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7158951	0.86[CHB][hapmap]
rs7159558	0.86[CHB][hapmap]
rs7160188	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7160195	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7975	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8007615	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8008449	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8009261	0.82[CHB][hapmap]
rs8009733	0.82[CHB][hapmap]
rs8016187	0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[EUR][1000 genomes];0.84[ASN][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	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv902105	chr14:77764884-77801431	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv902106	chr14:77767978-77801431	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2363643	GSTZ1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77785600-77789000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr14:77786400-77789000	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr14:77786600-77789000	Active TSS	NHLF	lung
4	chr14:77788200-77789000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:77788200-77789000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr14:77788200-77789000	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr14:77788200-77789000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr14:77788200-77789000	Flanking Active TSS	Liver	Liver
9	chr14:77788200-77789000	Flanking Active TSS	Dnd41	blood
10	chr14:77788200-77789000	Flanking Active TSS	NHEK	skin
11	chr14:77788200-77789200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr14:77788200-77789200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr14:77788200-77789200	Flanking Active TSS	Hela-S3	cervix
14	chr14:77788400-77789000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr14:77788400-77789000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr14:77788400-77789000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr14:77788400-77789000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr14:77788400-77789000	Flanking Active TSS	Brain Angular Gyrus	brain
19	chr14:77788400-77789000	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr14:77788400-77789000	Flanking Active TSS	Brain Substantia Nigra	brain
21	chr14:77788400-77789000	Enhancers	Lung	lung
22	chr14:77788400-77789000	Enhancers	Placenta Amnion	Placenta Amnion
23	chr14:77788400-77789000	Flanking Active TSS	Rectal Smooth Muscle	rectum
24	chr14:77788400-77789000	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr14:77788400-77789000	Flanking Active TSS	A549	lung
26	chr14:77788400-77789000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr14:77788400-77789000	Flanking Active TSS	NHDF-Ad	bronchial
28	chr14:77788400-77789200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr14:77788400-77789200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr14:77788400-77789200	Enhancers	Pancreas	Pancrea
31	chr14:77788400-77789200	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr14:77788400-77789400	Enhancers	Small Intestine	intestine
33	chr14:77788400-77790800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr14:77788600-77789000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr14:77788600-77789000	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr14:77788600-77789000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr14:77788600-77789000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr14:77788600-77789000	Enhancers	Primary T cells from cord blood	blood
39	chr14:77788600-77789000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr14:77788600-77789000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr14:77788600-77789000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr14:77788600-77789000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr14:77788600-77789000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr14:77788600-77789000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr14:77788600-77789000	Enhancers	Aorta	Aorta
46	chr14:77788600-77789000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr14:77788600-77789000	Enhancers	Fetal Kidney	kidney
48	chr14:77788600-77789000	Enhancers	Placenta	Placenta
49	chr14:77788600-77789000	Enhancers	Left Ventricle	heart
50	chr14:77788600-77789000	Enhancers	Rectal Mucosa Donor 31	rectum

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