Variant report

Variant	rs8009242
Chromosome Location	chr14:20799103-20799104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr14:20799085-20800048	SK-N-SH	brain:	n/a	n/a
2	YY1	chr14:20798938-20799106	K562	blood:	n/a	n/a
3	POLR2A	chr14:20798967-20799136	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOXA1	chr14:20799096-20799667	HepG2	liver:	n/a	chr14:20799371-20799383 chr14:20799625-20799637
5	MAX	chr14:20799074-20799685	HepG2	liver:	n/a	chr14:20799463-20799473
6	FOXA1	chr14:20799071-20799668	HepG2	liver:	n/a	chr14:20799371-20799383 chr14:20799625-20799637
7	POLR2A	chr14:20798484-20799220	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr14:20799096-20799727	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr14:20798464-20800154	K562	blood:	n/a	n/a
10	MXI1	chr14:20799076-20799658	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:20798864..20801597-chr14:20922807..20926169,3	K562	blood:
2	chr14:20798903..20803027-chr14:20936310..20943107,9	K562	blood:
3	chr14:20798903..20801469-chr14:20939189..20941712,2	K562	blood:

Variant related genes	Relation type
SNORD126	TF binding region
CCNB1IP1	TF binding region
ENSG00000092094	Chromatin interaction
ENSG00000198805	Chromatin interaction
ENSG00000100823	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10129957	0.86[CHB][hapmap]
rs10148359	0.81[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs10873395	0.85[CEU][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs11622655	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12891805	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1889362	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2297616	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2318864	0.80[CEU][hapmap];0.87[CHD][hapmap]
rs2700	0.86[CHB][hapmap];0.88[GIH][hapmap]
rs3093882	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3093890	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3093897	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3093900	0.81[ASN][1000 genomes]
rs3093902	0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3093904	0.84[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3093907	0.84[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs3093933	0.80[CEU][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs3093939	0.86[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs3093942	0.86[CHB][hapmap];0.80[JPT][hapmap];0.88[MEX][hapmap]
rs3742945	0.80[CEU][hapmap];0.87[CHD][hapmap]
rs4981150	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4981153	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4981158	0.94[MEX][hapmap];0.87[TSI][hapmap]
rs4981957	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4981983	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4981998	0.88[EUR][1000 genomes]
rs57101853	0.88[EUR][1000 genomes]
rs58530849	0.88[EUR][1000 genomes]
rs6575124	0.95[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6575135	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]
rs7152084	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7155699	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7161611	0.86[GIH][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap]
rs8014147	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8022565	1.00[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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8022671	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs878157	0.86[CHB][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs884368	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9323870	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs8009242	TTC5	cis	parietal	SCAN
rs8009242	TTC5	cis	cerebellum	SCAN
rs8009242	NDRG2	cis	parietal	SCAN
rs8009242	ZNF219	cis	cerebellum	SCAN
rs8009242	CCNB1IP1	cis	parietal	SCAN
rs8009242	PARP2	cis	parietal	SCAN
rs8009242	PARP2	cis	cerebellum	SCAN
rs8009242	CCNB1IP1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:20774200-20800400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr14:20774200-20800400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr14:20774200-20800400	Weak transcription	Fetal Brain Male	brain
4	chr14:20774200-20800400	Weak transcription	Stomach Mucosa	stomach
5	chr14:20774200-20800600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr14:20774200-20800800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr14:20774200-20800800	Weak transcription	Small Intestine	intestine
8	chr14:20782600-20800800	Weak transcription	Esophagus	oesophagus
9	chr14:20784800-20799200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr14:20785800-20800400	Weak transcription	Brain Hippocampus Middle	brain
11	chr14:20786200-20800600	Weak transcription	Aorta	Aorta
12	chr14:20786200-20800600	Weak transcription	Colonic Mucosa	Colon
13	chr14:20786400-20800800	Weak transcription	Pancreas	Pancrea
14	chr14:20787400-20800800	Weak transcription	Gastric	stomach
15	chr14:20787600-20800400	Weak transcription	Brain Germinal Matrix	brain
16	chr14:20790000-20800800	Weak transcription	Spleen	Spleen
17	chr14:20790600-20800800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr14:20793000-20800600	Weak transcription	Primary T cells from cord blood	blood
19	chr14:20793200-20799200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr14:20793200-20799600	Weak transcription	Brain Anterior Caudate	brain
21	chr14:20793200-20800200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr14:20793200-20800600	Weak transcription	Thymus	Thymus
23	chr14:20793200-20800800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr14:20793400-20800400	Weak transcription	Fetal Intestine Small	intestine
25	chr14:20793400-20800400	Weak transcription	Fetal Stomach	stomach
26	chr14:20793800-20800400	Weak transcription	Psoas Muscle	Psoas
27	chr14:20793800-20800600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr14:20793800-20800600	Weak transcription	Fetal Muscle Leg	muscle
29	chr14:20793800-20800600	Weak transcription	Lung	lung
30	chr14:20793800-20800600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr14:20793800-20800800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr14:20794800-20800400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr14:20794800-20800400	Weak transcription	Brain Substantia Nigra	brain
34	chr14:20794800-20800400	Weak transcription	Fetal Brain Female	brain
35	chr14:20794800-20800400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr14:20794800-20800600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr14:20794800-20800600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr14:20794800-20800600	Weak transcription	Placenta	Placenta
39	chr14:20795000-20800400	Weak transcription	Adipose Nuclei	Adipose
40	chr14:20795000-20800400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr14:20795000-20800400	Weak transcription	HSMMtube	muscle
42	chr14:20795000-20800600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr14:20795000-20800600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr14:20795000-20800600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr14:20795000-20800600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr14:20795200-20800400	Weak transcription	Fetal Lung	lung
47	chr14:20795200-20800600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr14:20795400-20800600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr14:20795400-20800600	Weak transcription	Fetal Thymus	thymus
50	chr14:20795600-20799400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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