Variant report

Variant	rs10065863
Chromosome Location	chr5:43604497-43604498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:43602425-43604573	HL-60	blood:	n/a	n/a
2	MXI1	chr5:43601361-43604702	SK-N-SH	brain:	n/a	n/a
3	SPI1	chr5:43604446-43604845	HL-60	blood:	n/a	chr5:43604676-43604683
4	MTA3	chr5:43601858-43604547	GM12878	blood:	n/a	n/a
5	TBL1XR1	chr5:43604490-43604532	K562	blood:	n/a	n/a
6	MAX	chr5:43603836-43604506	ECC-1	luminal epithelium:	n/a	chr5:43604385-43604394
7	POLR2A	chr5:43601962-43604666	PBDE	blood:	n/a	n/a
8	SPI1	chr5:43604473-43604853	HL-60	blood:	n/a	chr5:43604676-43604683

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:43554854..43559895-chr5:43599481..43606699,15	MCF-7	breast:
2	chr5:43482042..43485833-chr5:43601604..43604541,3	MCF-7	breast:
3	chr5:43512794..43515547-chr5:43602190..43604500,3	MCF-7	breast:
4	chr5:43604308..43606276-chr5:43607859..43609785,3	MCF-7	breast:
5	chr5:43555487..43559521-chr5:43598404..43605405,16	K562	blood:
6	chr5:43552832..43560830-chr5:43598877..43605844,26	MCF-7	breast:
7	chr5:43481246..43484731-chr5:43603166..43606245,4	K562	blood:
8	chr5:43482483..43486113-chr5:43601084..43606081,7	K562	blood:
9	chr5:43601763..43605743-chr5:43610640..43615837,7	K562	blood:
10	chr5:43555382..43559666-chr5:43598979..43604929,17	K562	blood:

No data

Variant related genes	Relation type
NNT-AS1	TF binding region
ENSG00000112992	Chromatin interaction
ENSG00000172244	Chromatin interaction
ENSG00000248240	Chromatin interaction
ENSG00000172239	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000151881	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10036954	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs10038608	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs10042992	0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs10055801	0.91[MEX][hapmap]
rs10057103	1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10058558	0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[ASN][1000 genomes]
rs10059993	0.96[MEX][hapmap]
rs10061165	0.87[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs10065689	0.96[MEX][hapmap]
rs10074682	0.85[CEU][hapmap];1.00[MEX][hapmap]
rs10447144	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10462051	0.85[CEU][hapmap]
rs1072745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1072746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10941640	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11949083	0.96[MEX][hapmap]
rs12521249	0.96[MEX][hapmap]
rs12652547	0.87[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs13189004	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13360902	0.84[ASN][1000 genomes]
rs1366410	0.96[MEX][hapmap]
rs1389868	0.85[CEU][hapmap]
rs1428640	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2172763	0.87[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs35881272	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs36013953	0.82[ASN][1000 genomes]
rs3776423	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs3806870	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs4072918	0.96[MEX][hapmap]
rs4072919	0.91[MEX][hapmap]
rs4073848	0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[ASN][1000 genomes]
rs4073850	0.81[ASN][1000 genomes]
rs4074777	0.96[MEX][hapmap]
rs4242099	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4367306	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4386738	0.96[MEX][hapmap]
rs4467713	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs4513704	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4535459	0.92[MEX][hapmap]
rs4610465	0.87[ASN][1000 genomes]
rs4866752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4866833	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs4991951	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55641556	0.83[ASN][1000 genomes]
rs56400900	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6451692	0.89[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs6451695	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs6451696	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs6451698	0.85[CEU][hapmap];0.83[MEX][hapmap]
rs6451706	0.87[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs6451718	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6860493	0.96[MEX][hapmap]
rs6862102	0.84[CEU][hapmap]
rs6870018	0.85[CEU][hapmap]
rs6878770	0.96[MEX][hapmap]
rs6883661	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6884661	0.96[MEX][hapmap]
rs6885679	0.96[MEX][hapmap]
rs6895327	0.96[MEX][hapmap]
rs6896693	0.96[MEX][hapmap]
rs750582	0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs750584	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7701429	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7703662	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs7708072	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7708369	0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7710125	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7710628	0.92[MEX][hapmap]
rs7713479	0.96[MEX][hapmap]
rs7715782	0.96[MEX][hapmap]
rs7718627	0.96[MEX][hapmap]
rs7724571	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7732656	0.96[MEX][hapmap]
rs7737793	0.87[ASN][1000 genomes]
rs9292883	0.82[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	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv830275	chr5:43469511-43639384	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
3	nsv881108	chr5:43527432-43800333	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10065863	YY2	trans	cerebellum	SCAN
rs10065863	C5orf34	cis	parietal	SCAN
rs10065863	MGC42105	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43600800-43604800	Active TSS	Psoas Muscle	Psoas
2	chr5:43600800-43605200	Active TSS	Right Atrium	heart
3	chr5:43601600-43604600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr5:43601800-43604600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:43601800-43604600	Active TSS	Fetal Brain Female	brain
6	chr5:43601800-43604800	Active TSS	Left Ventricle	heart
7	chr5:43602000-43604600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr5:43602000-43604600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:43602000-43604600	Active TSS	Aorta	Aorta
10	chr5:43602000-43604800	Active TSS	Right Ventricle	heart
11	chr5:43602200-43604600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:43602200-43604600	Active TSS	Fetal Stomach	stomach
13	chr5:43602400-43604600	Active TSS	H9 Cell Line	embryonic stem cell
14	chr5:43602400-43604600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:43602400-43604600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:43602400-43604600	Active TSS	Colonic Mucosa	Colon
17	chr5:43602400-43604800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:43602600-43604600	Active TSS	Fetal Intestine Large	intestine
19	chr5:43602600-43604600	Active TSS	Rectal Smooth Muscle	rectum
20	chr5:43602600-43604800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:43602600-43604800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:43602600-43604800	Active TSS	HSMM	muscle
23	chr5:43603400-43604600	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr5:43603400-43604800	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr5:43603400-43604800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr5:43603400-43604800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:43603400-43605000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr5:43603400-43605000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:43603600-43604600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:43603600-43604600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr5:43603600-43604600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:43603600-43604600	Flanking Active TSS	Hela-S3	cervix
33	chr5:43603600-43604600	Flanking Active TSS	HUVEC	blood vessel
34	chr5:43603600-43604600	Flanking Active TSS	K562	blood
35	chr5:43603600-43604600	Flanking Active TSS	NH-A	brain
36	chr5:43603600-43604600	Flanking Active TSS	NHEK	skin
37	chr5:43603600-43604800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
38	chr5:43603600-43604800	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr5:43603600-43605000	Flanking Active TSS	Liver	Liver
40	chr5:43603600-43605200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr5:43603800-43604600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:43603800-43604600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
43	chr5:43603800-43604600	Flanking Active TSS	Primary B cells from peripheral blood	blood
44	chr5:43603800-43604600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr5:43603800-43604600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:43603800-43604600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr5:43603800-43604600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr5:43603800-43604600	Flanking Active TSS	HepG2	liver
49	chr5:43603800-43604800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:43603800-43604800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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