Variant report

Variant	rs601060
Chromosome Location	chr1:47139580-47139581
allele	C/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	ATF1	chr1:47139412-47139784	K562	blood:	n/a	n/a
2	CUX1	chr1:47139440-47140063	K562	blood:	n/a	n/a
3	POLR2A	chr1:47139319-47139693	GM12891	blood:	n/a	n/a
4	JUN	chr1:47138728-47140546	K562	blood:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139608 chr1:47139598-47139607
5	JUND	chr1:47139320-47140026	SK-N-SH	brain:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139607 chr1:47139596-47139608 chr1:47139598-47139607
6	FOSL2	chr1:47139307-47139908	SK-N-SH	brain:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139597-47139608 chr1:47139596-47139608 chr1:47139598-47139607
7	MAFK	chr1:47139427-47139761	K562	blood:	n/a	chr1:47139599-47139608
8	ATF3	chr1:47139458-47139675	K562	blood:	n/a	n/a
9	POLR2A	chr1:47139309-47139708	HL-60	blood:	n/a	n/a
10	EP300	chr1:47139351-47139685	SK-N-SH_RA	brain:	n/a	chr1:47139597-47139606 chr1:47139598-47139607
11	POLR2A	chr1:47139413-47139631	GM12878	blood:	n/a	n/a
12	FOSL1	chr1:47139336-47139747	K562	blood:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139608 chr1:47139596-47139607 chr1:47139598-47139607
13	JUND	chr1:47139519-47139763	H1-hESC	embryonic stem cell:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139607 chr1:47139596-47139608 chr1:47139598-47139607
14	POLR2A	chr1:47139308-47139846	K562	blood:	n/a	n/a
15	TAL1	chr1:47139454-47139680	K562	blood:	n/a	n/a
16	JUND	chr1:47139474-47139642	HepG2	liver:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139607 chr1:47139596-47139608 chr1:47139598-47139607
17	FOSL1	chr1:47139400-47139734	K562	blood:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139608 chr1:47139596-47139607 chr1:47139598-47139607
18	JUND	chr1:47139327-47139829	K562	blood:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139607 chr1:47139596-47139608 chr1:47139598-47139607
19	FOXA1	chr1:47139436-47139717	HepG2	liver:	n/a	chr1:47139563-47139575
20	BHLHE40	chr1:47139449-47139955	K562	blood:	n/a	n/a
21	FOS	chr1:47139456-47139707	MCF10A-Er-Src	breast:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139607 chr1:47139596-47139608 chr1:47139598-47139607
22	JUND	chr1:47139475-47139690	HepG2	liver:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139607 chr1:47139596-47139608 chr1:47139598-47139607
23	EP300	chr1:47139430-47139714	SK-N-SH_RA	brain:	n/a	chr1:47139597-47139606 chr1:47139598-47139607
24	JUN	chr1:47139374-47139928	K562	blood:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139608 chr1:47139598-47139607
25	POLR2A	chr1:47138277-47140229	K562	blood:	n/a	n/a
26	MXI1	chr1:47139511-47139750	K562	blood:	n/a	n/a
27	FOS	chr1:47139457-47139773	MCF10A-Er-Src	breast:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139607 chr1:47139596-47139608 chr1:47139598-47139607
28	EP300	chr1:47139455-47139705	K562	blood:	n/a	chr1:47139597-47139606 chr1:47139598-47139607
29	PBX3	chr1:47139314-47139837	SK-N-SH	brain:	n/a	n/a
30	JUN	chr1:47139389-47139766	K562	blood:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139608 chr1:47139598-47139607
31	FOS	chr1:47139504-47139769	MCF10A-Er-Src	breast:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139607 chr1:47139596-47139608 chr1:47139598-47139607
32	JUN	chr1:47139411-47139755	HUVEC	blood vessel:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139608 chr1:47139598-47139607
33	FOS	chr1:47139521-47139743	MCF10A-Er-Src	breast:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139607 chr1:47139596-47139608 chr1:47139598-47139607
34	FOS	chr1:47139409-47139818	HUVEC	blood vessel:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139607 chr1:47139596-47139608 chr1:47139598-47139607
35	JUN	chr1:47139533-47139726	HepG2	liver:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139608 chr1:47139598-47139607
36	FOSL2	chr1:47139357-47139792	HepG2	liver:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139597-47139608 chr1:47139596-47139608 chr1:47139598-47139607
37	ZMIZ1	chr1:47139400-47139889	K562	blood:	n/a	n/a
38	POLR2A	chr1:47139278-47139688	K562	blood:	n/a	n/a
39	JUND	chr1:47139420-47139787	Hela-S3	cervix:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139607 chr1:47139596-47139608 chr1:47139598-47139607
40	POLR2A	chr1:47138978-47139899	HepG2	liver:	n/a	n/a
41	POLR2A	chr1:47138888-47139733	K562	blood:	n/a	n/a
42	GATA1	chr1:47138322-47140191	PBDE	blood:	n/a	n/a
43	FOS	chr1:47139400-47139789	K562	blood:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139607 chr1:47139596-47139608 chr1:47139598-47139607
44	FOSL2	chr1:47139360-47139770	HepG2	liver:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139597-47139608 chr1:47139596-47139608 chr1:47139598-47139607
45	ATF3	chr1:47139351-47139836	K562	blood:	n/a	n/a
46	POLR2A	chr1:47138753-47140039	Hela-S3	cervix:	n/a	n/a
47	JUND	chr1:47139439-47139775	HepG2	liver:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139607 chr1:47139596-47139608 chr1:47139598-47139607
48	JUND	chr1:47139285-47139874	SK-N-SH	brain:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139607 chr1:47139596-47139608 chr1:47139598-47139607
49	POLR2A	chr1:47139279-47139629	K562	blood:	n/a	n/a
50	JUN	chr1:47139346-47139778	K562	blood:	n/a	chr1:47139599-47139606 chr1:47139597-47139607 chr1:47139598-47139606 chr1:47139596-47139608 chr1:47139598-47139607

No.	Distal block	Cell Line	Cell type
1	chr1:47133631..47136554-chr1:47137710..47141962,4	K562	blood:
2	chr1:47130612..47137538-chr1:47138503..47143012,9	K562	blood:
3	chr1:47134287..47136852-chr1:47138117..47139620,2	MCF-7	breast:

Variant related genes	Relation type
ATPAF1	TF binding region
EFCAB14-AS1	TF binding region
ENSG00000186118	Chromatin interaction
ENSG00000233647	Chromatin interaction
ENSG00000123472	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10749863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749864	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258061	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12794	0.91[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];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1371834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473292	0.90[YRI][hapmap]
rs1545206	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595898	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1816730	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs1866770	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890473	0.91[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083485	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099766	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2165317	0.90[YRI][hapmap]
rs2218191	0.94[EUR][1000 genomes]
rs2476158	0.92[EUR][1000 genomes]
rs35050319	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35861275	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4097354	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4553120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660359	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4660954	0.90[YRI][hapmap]
rs4660956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618505	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6668899	0.84[ASN][1000 genomes]
rs7516616	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547522	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS 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 miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs601060	ATPAF1	cis	multi-tissue	Pritchard
rs601060	EFCAB14	cis	Whole Blood	GTEx
rs601060	EFCAB14	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47134400-47140400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:47134400-47145800	Weak transcription	Hela-S3	cervix
3	chr1:47134400-47147800	Weak transcription	Small Intestine	intestine
4	chr1:47134600-47139600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr1:47134600-47139600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:47134600-47139600	Weak transcription	Stomach Mucosa	stomach
7	chr1:47134600-47139600	Weak transcription	HSMM	muscle
8	chr1:47134600-47139600	Weak transcription	Osteobl	bone
9	chr1:47134600-47139800	Weak transcription	NHLF	lung
10	chr1:47134600-47140800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:47134600-47141200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:47134600-47141200	Weak transcription	Aorta	Aorta
13	chr1:47134600-47141200	Weak transcription	HepG2	liver
14	chr1:47134600-47141400	Weak transcription	NH-A	brain
15	chr1:47134600-47142600	Weak transcription	HSMMtube	muscle
16	chr1:47134600-47142800	Weak transcription	Ovary	ovary
17	chr1:47134600-47143000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:47134600-47143200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:47134600-47145600	Weak transcription	Fetal Kidney	kidney
20	chr1:47134600-47145800	Weak transcription	Fetal Brain Male	brain
21	chr1:47134600-47147000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:47134600-47147800	Weak transcription	Psoas Muscle	Psoas
23	chr1:47134600-47149200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:47134600-47153000	Weak transcription	Right Atrium	heart
25	chr1:47134600-47157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:47134800-47139600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:47134800-47139600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:47134800-47141000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:47134800-47141000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:47134800-47141000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:47134800-47141000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:47134800-47141000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:47134800-47141000	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:47134800-47141000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:47134800-47141200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:47134800-47141200	Weak transcription	Brain Substantia Nigra	brain
37	chr1:47134800-47141200	Weak transcription	Right Ventricle	heart
38	chr1:47134800-47142800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:47134800-47142800	Weak transcription	Fetal Lung	lung
40	chr1:47134800-47143000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:47134800-47143200	Weak transcription	Brain Angular Gyrus	brain
42	chr1:47134800-47152600	Weak transcription	A549	lung
43	chr1:47135000-47139600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:47135000-47139600	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr1:47135000-47139600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:47135000-47139600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:47135000-47141000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:47135000-47141000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:47135000-47141400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr1:47135000-47142400	Weak transcription	HMEC	breast

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