Variant report

Variant	rs6575135
Chromosome Location	chr14:20787961-20787962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:20787855-20788231	HepG2	liver:	n/a	n/a
2	POLR2A	chr14:20787851-20788259	HepG2	liver:	n/a	n/a
3	POLR2A	chr14:20784055-20788798	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr14:20787939-20788232	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr14:20787219-20788700	K562	blood:	n/a	n/a
6	POLR2A	chr14:20787824-20788119	K562	blood:	n/a	n/a
7	FAM48A	chr14:20787804-20787964	GM12878	blood:	n/a	n/a
8	POLR2A	chr14:20787764-20788287	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr14:20787779-20788178	K562	blood:	n/a	n/a
10	POLR2A	chr14:20787545-20788532	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr14:20786919..20788985-chr14:20810151..20813024,2	MCF-7	breast:
2	chr14:20786888..20790712-chr14:20796897..20800765,3	K562	blood:
3	chr14:20787923..20789445-chr14:20794092..20796187,2	K562	blood:
4	chr14:20787309..20789953-chr14:20789984..20791962,2	MCF-7	breast:

No data

Variant related genes	Relation type
CCNB1IP1	TF binding region
ENSG00000259001	Chromatin interaction
ENSG00000100814	Chromatin interaction
ENSG00000238344	Chromatin interaction
ENSG00000222489	Chromatin interaction
ENSG00000129484	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10129957	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs10147163	0.81[CEU][hapmap]
rs10148359	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs10873395	0.81[CEU][hapmap];0.95[CHD][hapmap];0.81[ASN][1000 genomes]
rs11622655	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12891805	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1889362	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297616	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2318864	0.91[CHD][hapmap]
rs2700	0.86[CHB][hapmap];0.88[GIH][hapmap]
rs3093882	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3093890	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3093897	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3093902	0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3093904	0.90[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3093907	0.84[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs3093933	0.85[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs3093939	0.81[CEU][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs3093942	0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap]
rs3742945	0.91[CHD][hapmap]
rs4981150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981153	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981158	0.81[CEU][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs4981957	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4981983	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4981998	0.87[EUR][1000 genomes]
rs57101853	0.87[EUR][1000 genomes]
rs58530849	0.87[EUR][1000 genomes]
rs6575124	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7152084	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7155699	0.90[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7161611	0.81[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs8009242	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][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[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8014147	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8022565	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8022671	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs878157	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs884368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323870	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043923	chr14:20338742-21336425	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
2	nsv541970	chr14:20338742-21336425	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
3	nsv1037160	chr14:20517485-20901811	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
4	nsv541974	chr14:20517485-20901811	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
5	esv1806993	chr14:20743269-20841162	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
6	nsv534131	chr14:20757405-20886235	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1042025	chr14:20787961-20817851	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6575135	NDRG2	cis	parietal	SCAN
rs6575135	PARP2	cis	multi-tissue	Pritchard
rs6575135	TTC5	cis	parietal	SCAN
rs6575135	TTC5	cis	cerebellum	SCAN
rs6575135	RPPH1	cis	multi-tissue	Pritchard
rs6575135	PARP2	cis	cerebellum	SCAN
rs6575135	CCNB1IP1	cis	parietal	SCAN
rs6575135	CCNB1IP1	cis	cerebellum	SCAN
rs6575135	ZNF219	cis	cerebellum	SCAN
rs6575135	PARP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:20774200-20795400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr14:20774200-20795600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr14:20774200-20795600	Weak transcription	Fetal Heart	heart
4	chr14:20774200-20800400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr14:20774200-20800400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr14:20774200-20800400	Weak transcription	Fetal Brain Male	brain
7	chr14:20774200-20800400	Weak transcription	Stomach Mucosa	stomach
8	chr14:20774200-20800600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr14:20774200-20800800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr14:20774200-20800800	Weak transcription	Small Intestine	intestine
11	chr14:20778800-20798600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr14:20779000-20795600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr14:20779400-20788400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr14:20779400-20788600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr14:20779400-20788800	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr14:20779400-20788800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr14:20779400-20790200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr14:20779400-20794000	Strong transcription	Left Ventricle	heart
19	chr14:20779400-20794200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr14:20779400-20794800	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr14:20779400-20794800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr14:20779400-20795000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr14:20779400-20795000	Strong transcription	Osteobl	bone
24	chr14:20779400-20795200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr14:20779400-20795200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr14:20779400-20795400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr14:20779400-20797000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr14:20779400-20797200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr14:20779400-20797800	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr14:20779400-20798000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr14:20779400-20799000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr14:20779600-20788400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr14:20779600-20788600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr14:20779600-20788600	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr14:20779600-20788600	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr14:20779600-20788600	Strong transcription	HSMM	muscle
37	chr14:20779600-20788800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr14:20779600-20788800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr14:20779600-20788800	Strong transcription	Adipose Nuclei	Adipose
40	chr14:20779600-20789000	Strong transcription	Fetal Muscle Leg	muscle
41	chr14:20779600-20789400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr14:20779600-20789800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr14:20779600-20790800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr14:20779600-20793000	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr14:20779600-20793200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr14:20779600-20794800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr14:20779600-20794800	Strong transcription	HepG2	liver
48	chr14:20779600-20795000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr14:20779600-20795000	Strong transcription	Liver	Liver
50	chr14:20779600-20795000	Strong transcription	Dnd41	blood

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