Variant report

Variant	rs2295997
Chromosome Location	chr1:45293752-45293753
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:45291776-45293815	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45293445..45296144-chr1:45327310..45329571,2	K562	blood:
2	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
3	chr1:45293740..45296221-chr1:45811017..45813846,2	K562	blood:
4	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
5	chr1:45292689..45295107-chr1:45479598..45481361,2	K562	blood:
6	chr1:45293211..45295000-chr1:45954094..45956498,2	K562	blood:
7	chr1:45293006..45294513-chr1:45507730..45509268,2	K562	blood:
8	chr1:45293029..45295076-chr1:45769453..45771554,2	MCF-7	breast:
9	chr1:45203979..45206938-chr1:45293246..45295572,3	MCF-7	breast:
10	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:
11	chr1:45292499..45294385-chr1:45295727..45297570,3	MCF-7	breast:

No data

Variant related genes	Relation type
PTCH2	TF binding region
ENSG00000200169	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000234093	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000142959	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10890313	0.92[CEU][hapmap]
rs11211025	0.92[CEU][hapmap]
rs11211026	0.92[CEU][hapmap];0.80[TSI][hapmap]
rs11211036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11211040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211045	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211048	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211051	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211053	0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1140279	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.85[ASN][1000 genomes]
rs11556200	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs11573542	0.97[ASN][1000 genomes]
rs11573557	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11573559	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11573562	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11573592	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578233	0.83[ASN][1000 genomes]
rs11580010	0.83[ASN][1000 genomes]
rs11582718	0.83[ASN][1000 genomes]
rs11584440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11801990	0.95[CHB][hapmap]
rs11803622	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs11806832	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11809931	0.88[ASN][1000 genomes]
rs12125367	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs12126314	0.81[JPT][hapmap]
rs12126318	0.82[JPT][hapmap]
rs12126557	0.84[CEU][hapmap]
rs12139143	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566610	0.84[ASN][1000 genomes]
rs12569156	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12723764	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12729917	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12732939	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs12733586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12733796	0.84[ASN][1000 genomes]
rs12735038	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12735637	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs12738360	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12741443	0.86[ASN][1000 genomes]
rs12746270	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]
rs12749130	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs12755554	0.82[JPT][hapmap]
rs16832210	0.82[CEU][hapmap]
rs16832227	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs16832263	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16832265	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17881698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17883049	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17886118	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2295998	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2295999	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs263989	0.82[CHD][hapmap]
rs264022	0.82[CHD][hapmap]
rs264025	0.82[CHD][hapmap]
rs34436945	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34506400	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34541568	0.87[ASN][1000 genomes]
rs34639510	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34984079	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35343809	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35932693	0.81[ASN][1000 genomes]
rs35957134	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs364482	0.82[CHD][hapmap]
rs3795713	0.85[ASN][1000 genomes]
rs3795714	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs3795719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820586	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.90[TSI][hapmap];0.83[ASN][1000 genomes]
rs4342887	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]
rs4399199	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs57139686	0.81[ASN][1000 genomes]
rs57995027	0.83[ASN][1000 genomes]
rs59366549	0.83[ASN][1000 genomes]
rs6429549	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6429550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6670449	0.84[ASN][1000 genomes]
rs6676749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6689911	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]
rs6692487	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6692713	0.82[JPT][hapmap]
rs6695350	0.84[ASN][1000 genomes]
rs6697153	0.88[ASN][1000 genomes]
rs6702415	0.84[ASN][1000 genomes]
rs6703452	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6704436	0.84[ASN][1000 genomes]
rs67408784	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67742332	0.84[ASN][1000 genomes]
rs7517439	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7517639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7527787	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7528461	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7531019	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7534487	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7536078	0.94[CHB][hapmap]
rs7546285	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7553658	0.81[JPT][hapmap]

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	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
8	nsv546146	chr1:45258141-45318752	Genic enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	109 gene(s)	inside rSNPs	diseases
9	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2295997	UROD	cis	Artery Tibial	GTEx
rs2295997	SNORD55	cis	parietal	SCAN
rs2295997	ZNF691	cis	cerebellum	SCAN
rs2295997	UROD	cis	Adipose Subcutaneous	GTEx
rs2295997	UROD	cis	lung	GTEx
rs2295997	EIF2B3	cis	cerebellum	SCAN
rs2295997	SNORD55	cis	cerebellum	SCAN
rs2295997	TIE1	cis	parietal	SCAN
rs2295997	BEST4	cis	lymphoblastoid	seeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45286200-45301800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:45286400-45308400	Weak transcription	Aorta	Aorta
3	chr1:45286600-45299400	Weak transcription	Primary B cells from cord blood	blood
4	chr1:45286600-45301600	Weak transcription	Right Atrium	heart
5	chr1:45286600-45301800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:45286800-45301600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:45287000-45301800	Weak transcription	Thymus	Thymus
8	chr1:45287200-45293800	Weak transcription	Fetal Lung	lung
9	chr1:45287200-45295000	Weak transcription	Brain Substantia Nigra	brain
10	chr1:45287200-45307400	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:45289400-45307600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:45291800-45295200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:45291800-45295400	Strong transcription	Fetal Brain Female	brain
14	chr1:45291800-45295800	Strong transcription	Brain Germinal Matrix	brain
15	chr1:45291800-45297000	Strong transcription	Ovary	ovary
16	chr1:45291800-45298800	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr1:45292000-45293800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:45292200-45294200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:45292200-45294200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:45292200-45295600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:45292200-45296000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:45292200-45301800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr1:45292400-45294400	Strong transcription	Brain Anterior Caudate	brain
24	chr1:45292400-45294800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:45292400-45296800	Weak transcription	Stomach Mucosa	stomach
26	chr1:45292400-45297200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:45292400-45297200	Weak transcription	Colonic Mucosa	Colon
28	chr1:45292400-45308200	Weak transcription	Rectal Smooth Muscle	rectum
29	chr1:45292600-45293800	Enhancers	Duodenum Mucosa	Duodenum
30	chr1:45292600-45294200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:45292600-45294800	Weak transcription	Right Ventricle	heart
32	chr1:45292600-45295000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:45292600-45297200	Strong transcription	Fetal Stomach	stomach
34	chr1:45292600-45297400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:45292800-45293800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:45292800-45294400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:45292800-45294600	Weak transcription	Lung	lung
38	chr1:45292800-45295400	Weak transcription	Fetal Thymus	thymus
39	chr1:45292800-45295600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:45292800-45295600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:45292800-45295600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:45292800-45296000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr1:45292800-45297200	Weak transcription	Spleen	Spleen
44	chr1:45292800-45301400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:45293000-45294600	Strong transcription	Fetal Muscle Leg	muscle
46	chr1:45293000-45295000	Weak transcription	Placenta	Placenta
47	chr1:45293000-45295400	Weak transcription	K562	blood
48	chr1:45293000-45295600	Weak transcription	Adipose Nuclei	Adipose
49	chr1:45293000-45301400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:45293000-45301800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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