Variant report

Variant	rs4342887
Chromosome Location	chr1:45224998-45224999
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45224617-45225227	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr1:45224794-45225094	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:45224410-45227043	K562	blood:	n/a	n/a
4	POLR2A	chr1:45224566-45227109	K562	blood:	n/a	n/a
5	JUND	chr1:45224835-45225132	HepG2	liver:	n/a	chr1:45225021-45225032
6	JUN	chr1:45224904-45225073	HepG2	liver:	n/a	chr1:45225021-45225032 chr1:45224977-45224990
7	POLR2A	chr1:45224569-45225851	HL-60	blood:	n/a	n/a
8	POLR2A	chr1:45224405-45227009	K562	blood:	n/a	n/a
9	POLR2A	chr1:45224769-45225049	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:45224555-45226798	K562	blood:	n/a	n/a
11	POLR2A	chr1:45224663-45225087	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:45224471-45227096	K562	blood:	n/a	n/a
13	POLR2A	chr1:45224997-45225311	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:45224561-45227047	K562	blood:	n/a	n/a
15	POLR2A	chr1:45224721-45225024	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr1:45224785-45225026	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:45224240..45226290-chr1:45308445..45310205,2	K562	blood:
2	chr1:45185599..45189940-chr1:45221771..45225524,5	MCF-7	breast:
3	chr1:45223594..45225886-chr1:45284198..45286791,2	K562	blood:
4	chr1:45171946..45173521-chr1:45223386..45225623,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BEST4-1	chr1:45224796-45225014	ENSG00000225721.1
2	lnc-BEST4-1	chr1:45224709-45225014	ENSG00000225721.1

No data

Variant related genes	Relation type
KIF2C	TF binding region
ENSG00000226499	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10890313	0.93[CEU][hapmap];0.84[TSI][hapmap]
rs11211025	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs11211026	0.93[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs11211036	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11211038	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11211040	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs11211045	0.84[ASN][1000 genomes]
rs11211048	0.84[ASN][1000 genomes]
rs11211051	0.81[ASN][1000 genomes]
rs11211053	0.93[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap]
rs1140279	0.82[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11573542	0.83[ASN][1000 genomes]
rs11573557	0.81[ASN][1000 genomes]
rs11573559	0.81[ASN][1000 genomes]
rs11573562	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs11573592	0.85[ASN][1000 genomes]
rs11578233	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11580010	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11580159	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11582718	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11584440	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11800505	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11801990	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs11803622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11806832	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11809931	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12125367	0.85[CHD][hapmap]
rs12126557	0.84[CEU][hapmap]
rs12139143	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.80[ASN][1000 genomes]
rs12566610	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12569156	0.84[ASN][1000 genomes]
rs12723764	0.84[ASN][1000 genomes]
rs12729917	0.81[ASN][1000 genomes]
rs12732939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12733586	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs12733796	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12735038	0.84[ASN][1000 genomes]
rs12735637	0.85[CHD][hapmap]
rs12735728	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12738360	0.84[ASN][1000 genomes]
rs12741443	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12746270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12746898	0.83[EUR][1000 genomes]
rs16832227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16832263	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.81[ASN][1000 genomes]
rs16832265	0.84[ASN][1000 genomes]
rs17881698	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17883049	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17886118	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2295997	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.90[TSI][hapmap];0.85[ASN][1000 genomes]
rs2295998	0.85[ASN][1000 genomes]
rs2295999	0.85[ASN][1000 genomes]
rs34436945	0.81[ASN][1000 genomes]
rs34541568	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34639510	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34984079	0.85[ASN][1000 genomes]
rs35343809	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35932693	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35957134	0.84[ASN][1000 genomes]
rs3795713	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795719	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3820586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57995027	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59366549	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59788723	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6429549	0.85[ASN][1000 genomes]
rs6429550	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6670449	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6676749	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6689911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692487	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6695350	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6697153	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6702415	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6703452	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.80[ASN][1000 genomes]
rs6704436	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67408784	0.85[ASN][1000 genomes]
rs67742332	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517439	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs7517639	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7527787	0.85[ASN][1000 genomes]
rs7528461	0.84[ASN][1000 genomes]
rs7534487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7536078	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7539538	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7546285	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases
8	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4342887	SNORD55	cis	parietal	SCAN
rs4342887	UROD	cis	lung	GTEx
rs4342887	BEST4	cis	lymphoblastoid	seeQTL
rs4342887	SNORD55	cis	cerebellum	SCAN
rs4342887	EIF2B3	cis	cerebellum	SCAN
rs4342887	FOXJ3	cis	parietal	SCAN
rs4342887	ZNF691	cis	cerebellum	SCAN
rs4342887	UROD	cis	Artery Tibial	GTEx
rs4342887	TIE1	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45205800-45240600	Weak transcription	Ovary	ovary
2	chr1:45206000-45240400	Weak transcription	Right Atrium	heart
3	chr1:45206200-45225800	Weak transcription	Primary T cells from cord blood	blood
4	chr1:45206200-45227400	Weak transcription	Colonic Mucosa	Colon
5	chr1:45206200-45230200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:45206200-45240400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:45206200-45240600	Weak transcription	Stomach Mucosa	stomach
8	chr1:45206400-45232800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:45206400-45240600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr1:45206600-45240600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:45206800-45226600	Weak transcription	Fetal Brain Male	brain
12	chr1:45206800-45240200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:45207000-45233800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:45207200-45234200	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr1:45207200-45234400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:45207400-45233800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:45207600-45233800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:45207600-45234400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:45208600-45233400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:45208600-45234000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:45208800-45234400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:45209400-45235200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:45211200-45233800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:45211400-45229400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:45211400-45233600	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr1:45211400-45234800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:45211400-45235000	Strong transcription	Fetal Stomach	stomach
28	chr1:45211600-45231200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:45211600-45234600	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:45211600-45235200	Strong transcription	Thymus	Thymus
31	chr1:45211800-45229400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:45211800-45229400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:45212000-45235000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:45212000-45235200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:45212400-45234800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:45212400-45235000	Strong transcription	Fetal Thymus	thymus
37	chr1:45214400-45240400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:45215200-45231000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:45215600-45233600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:45215800-45226400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:45216600-45226000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:45217800-45229800	Strong transcription	K562	blood
43	chr1:45217800-45233400	Strong transcription	Fetal Intestine Small	intestine
44	chr1:45218000-45229400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr1:45218000-45240600	Weak transcription	Small Intestine	intestine
46	chr1:45218200-45229400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:45218200-45229400	Strong transcription	HSMM	muscle
48	chr1:45218200-45229800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:45218200-45229800	Strong transcription	NHLF	lung
50	chr1:45218200-45230000	Strong transcription	Osteobl	bone

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