Variant report

Variant	rs60292279
Chromosome Location	chr1:75199615-75199616
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:314)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:314 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:75199500-75199650	HMF	breast:	n/a	n/a
2	CTCF	chr1:75199500-75199650	HL-60	blood:	n/a	n/a
3	CTCF	chr1:75199480-75199630	HPF	lung:	n/a	n/a
4	CTCF	chr1:75199520-75199670	WERI-Rb-1	eye:	n/a	n/a
5	CUX1	chr1:75198508-75199670	K562	blood:	n/a	n/a
6	RAD21	chr1:75199354-75199738	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:75199329-75199620	GM12891	blood:	n/a	n/a
8	MYC	chr1:75198487-75199709	MCF10A-Er-Src	breast:	n/a	n/a
9	CTCF	chr1:75199480-75199630	HFF-Myc	foreskin:	n/a	n/a
10	POLR2A	chr1:75198636-75200123	IMR90	lung:	n/a	n/a
11	RELA	chr1:75196976-75199695	GM19193	blood:	n/a	n/a
12	CTCF	chr1:75199444-75199722	Medullo	brain:	n/a	n/a
13	FOS	chr1:75199409-75200096	MCF10A-Er-Src	breast:	n/a	n/a
14	CEBPB	chr1:75198629-75199853	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr1:75199459-75199702	LNCaP	prostate:	n/a	n/a
16	HCFC1	chr1:75198603-75199689	K562	blood:	n/a	n/a
17	MXI1	chr1:75198396-75199698	HepG2	liver:	n/a	n/a
18	CTCF	chr1:75199480-75199630	HEK293	kidney:	n/a	n/a
19	CTCF	chr1:75199480-75199630	BE2_C	brain:	n/a	n/a
20	TBP	chr1:75198394-75199677	H1-hESC	embryonic stem cell:	n/a	n/a
21	RELA	chr1:75197065-75199714	GM15510	blood:	n/a	n/a
22	ATF1	chr1:75199418-75199743	K562	blood:	n/a	n/a
23	KAP1	chr1:75199458-75199669	K562	blood:	n/a	n/a
24	POLR2A	chr1:75198271-75199697	K562	blood:	n/a	n/a
25	MAZ	chr1:75198620-75199645	HepG2	liver:	n/a	n/a
26	CTCF	chr1:75199520-75199670	HRPEpiC	eye:	n/a	n/a
27	CTCF	chr1:75199500-75199650	Hela-S3	cervix:	n/a	n/a
28	MXI1	chr1:75198512-75199712	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr1:75199371-75199662	GM12891	blood:	n/a	n/a
30	CTCF	chr1:75199358-75199742	K562	blood:	n/a	n/a
31	CTCF	chr1:75199480-75199630	RPTEC	kidney:	n/a	n/a
32	CTCF	chr1:75199520-75199670	HFF	foreskin:	n/a	n/a
33	CTCF	chr1:75199459-75199664	HepG2	liver:	n/a	n/a
34	POLR2A	chr1:75198510-75199668	Hela-S3	cervix:	n/a	n/a
35	BACH1	chr1:75199266-75200027	K562	blood:	n/a	n/a
36	POLR2A	chr1:75198317-75199727	GM12892	blood:	n/a	n/a
37	CTCF	chr1:75199431-75199696	Hela-S3	cervix:	n/a	n/a
38	FOXM1	chr1:75198400-75199698	GM12878	blood:	n/a	n/a
39	YY1	chr1:75198507-75199675	SK-N-SH_RA	brain:	n/a	chr1:75198846-75198868
40	POLR2A	chr1:75198430-75199823	MCF10A-Er-Src	breast:	n/a	n/a
41	CTCF	chr1:75199416-75199623	T-47D	breast:	n/a	n/a
42	CTCF	chr1:75199456-75199665	MCF-7	breast:	n/a	n/a
43	CTCF	chr1:75199453-75199683	Pancreas_OC	pancreas:	n/a	n/a
44	CTCF	chr1:75199500-75199650	GM12870	blood:	n/a	n/a
45	RCOR1	chr1:75198071-75199802	GM12878	blood:	n/a	n/a
46	MAX	chr1:75198301-75199808	HepG2	liver:	n/a	n/a
47	CTCF	chr1:75199425-75199658	SK-N-SH_RA	brain:	n/a	n/a
48	CTCF	chr1:75199480-75199630	HMF	breast:	n/a	n/a
49	CTCF	chr1:75199500-75199650	Caco-2	colon:	n/a	n/a
50	RELA	chr1:75197077-75199725	GM12891	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:75197640..75200637-chr1:75200867..75204722,5	MCF-7	breast:
2	chr1:75182455..75184516-chr1:75199218..75200932,2	K562	blood:
3	chr1:75197237..75200127-chr1:76254006..76255529,2	K562	blood:
4	chr1:75197578..75200968-chr1:75201632..75206969,6	MCF-7	breast:
5	chr1:74977554..74979985-chr1:75198825..75201036,2	K562	blood:
6	chr1:74969628..74970367-chr1:75199475..75200023,2	MCF-7	breast:

No data

Variant related genes	Relation type
TYW3	TF binding region
CRYZ	TF binding region
ENSG00000162621	Chromatin interaction
ENSG00000162623	Chromatin interaction
ENSG00000201487	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11162945	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1122338	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1133891	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11485264	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11485299	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12034724	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12043726	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13375787	0.82[AMR][1000 genomes]
rs1359750	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1581870	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2032969	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28374065	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28436025	0.82[AMR][1000 genomes]
rs28445096	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28515016	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28563168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28575168	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28719150	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28740807	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28804147	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28810187	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806161	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3819946	0.86[AMR][1000 genomes]
rs3819947	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4650004	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4650007	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4650287	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4650288	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58715708	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6681874	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67696801	0.82[AMR][1000 genomes]
rs745108	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535692	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7540514	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs768223	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9647	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv830259	chr1:75089177-75241062	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv1851105	chr1:75152186-75302921	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv546579	chr1:75197533-75200486	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs60292279	TYW3	cis	Artery Tibial	GTEx
rs60292279	TYW3	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75195600-75200400	Active TSS	A549	lung
2	chr1:75196800-75200000	Active TSS	Fetal Intestine Large	intestine
3	chr1:75197200-75199800	Active TSS	Colonic Mucosa	Colon
4	chr1:75197200-75200000	Active TSS	Right Atrium	heart
5	chr1:75197200-75200400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr1:75197400-75200000	Active TSS	Osteobl	bone
7	chr1:75197600-75199800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:75197600-75199800	Active TSS	Aorta	Aorta
9	chr1:75197600-75200000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:75197600-75200000	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr1:75197600-75200000	Active TSS	Muscle Satellite Cultured Cells	--
12	chr1:75197600-75200000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:75197600-75200200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:75197600-75200200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:75197600-75200200	Active TSS	Ovary	ovary
16	chr1:75197600-75200400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:75197600-75200600	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr1:75197800-75199800	Active TSS	NHEK	skin
19	chr1:75197800-75200000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:75197800-75200000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:75197800-75200200	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr1:75197800-75200200	Active TSS	NHDF-Ad	bronchial
23	chr1:75197800-75200800	Active TSS	NHLF	lung
24	chr1:75197800-75201800	Active TSS	GM12878-XiMat	blood
25	chr1:75198000-75199800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:75198000-75199800	Active TSS	Brain Hippocampus Middle	brain
27	chr1:75198000-75199800	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr1:75198000-75199800	Active TSS	Brain Substantia Nigra	brain
29	chr1:75198000-75199800	Active TSS	Fetal Brain Female	brain
30	chr1:75198000-75199800	Active TSS	HSMM	muscle
31	chr1:75198000-75200000	Active TSS	H1 Cell Line	embryonic stem cell
32	chr1:75198000-75200000	Active TSS	H9 Cell Line	embryonic stem cell
33	chr1:75198000-75200000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:75198000-75200000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:75198000-75200000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:75198000-75200000	Active TSS	Brain Germinal Matrix	brain
37	chr1:75198000-75200000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:75198000-75200000	Active TSS	HMEC	breast
39	chr1:75198000-75200000	Active TSS	K562	blood
40	chr1:75198000-75200200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:75198000-75200200	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr1:75198000-75200600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:75198200-75199800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:75198200-75199800	Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr1:75198200-75199800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr1:75198200-75199800	Active TSS	Fetal Muscle Leg	muscle
47	chr1:75198200-75199800	Active TSS	Right Ventricle	heart
48	chr1:75198200-75199800	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr1:75198200-75199800	Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr1:75198200-75199800	Active TSS	Thymus	Thymus

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