Variant report

Variant	rs7474070
Chromosome Location	chr1:171050589-171050590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:125)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:125 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:171050500-171050650	NHEK	skin:	n/a	n/a
2	CTCF	chr1:171050500-171050650	HCFaa	heart:	n/a	n/a
3	CTCF	chr1:171050480-171050630	HCM	heart:	n/a	n/a
4	RAD21	chr1:171050311-171050811	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr1:171050454-171050665	HUVEC	blood vessel:	n/a	n/a
6	CTCF	chr1:171050516-171050658	MCF-7	breast:	n/a	n/a
7	RAD21	chr1:171050418-171050765	HepG2	liver:	n/a	n/a
8	CTCF	chr1:171050560-171050710	HEK293	kidney:	n/a	n/a
9	CTCF	chr1:171050580-171050730	WI-38	lung:	n/a	n/a
10	CTCF	chr1:171050460-171050610	GM12864	blood:	n/a	n/a
11	CTCF	chr1:171050480-171050630	AG04449	skin:	n/a	n/a
12	CTCF	chr1:171050459-171050636	A549	lung:	n/a	n/a
13	CTCF	chr1:171050480-171050630	HBMEC	blood vessel:	n/a	n/a
14	CTCF	chr1:171050500-171050650	HVMF	connective:	n/a	n/a
15	SMC3	chr1:171050310-171050787	SK-N-SH	brain:	n/a	n/a
16	CTCF	chr1:171050459-171050667	LNCaP	prostate:	n/a	n/a
17	CTCF	chr1:171050480-171050630	MCF-7	breast:	n/a	n/a
18	CTCF	chr1:171050548-171050627	Gliobla	brain:	n/a	n/a
19	CTCF	chr1:171050517-171050596	GM13977	blood:	n/a	n/a
20	CTCF	chr1:171050500-171050650	AG10803	skin:	n/a	n/a
21	CTCF	chr1:171050500-171050650	NHDF-neo	bronchial:	n/a	n/a
22	USF1	chr1:171050578-171050972	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr1:171050474-171050683	SK-N-SH_RA	brain:	n/a	n/a
24	CTCF	chr1:171050498-171050614	GM10266	blood:	n/a	n/a
25	CTCF	chr1:171050353-171050779	IMR90	lung:	n/a	n/a
26	KAP1	chr1:171050493-171050923	HEK293	kidney:	n/a	n/a
27	CTCF	chr1:171050460-171050610	RPTEC	kidney:	n/a	n/a
28	CTCF	chr1:171050460-171050610	HBMEC	blood vessel:	n/a	n/a
29	CTCF	chr1:171050480-171050630	HUVEC	blood vessel:	n/a	n/a
30	RAD21	chr1:171050435-171050748	A549	lung:	n/a	n/a
31	CTCF	chr1:171050520-171050670	SAEC	small airway:	n/a	n/a
32	CTCF	chr1:171050520-171050670	BJ	skin:	n/a	n/a
33	CTCF	chr1:171050460-171050610	Hela-S3	cervix:	n/a	n/a
34	RAD21	chr1:171050456-171050714	GM12878	blood:	n/a	n/a
35	CTCF	chr1:171050480-171050648	GM12878	blood:	n/a	n/a
36	CTCF	chr1:171050520-171050670	AG04450	lung:	n/a	n/a
37	RAD21	chr1:171050415-171050769	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr1:171050500-171050650	AG04450	lung:	n/a	n/a
39	RAD21	chr1:171050402-171050741	GM12878	blood:	n/a	n/a
40	CTCF	chr1:171050397-171050734	HCT-116	colon:	n/a	n/a
41	RAD21	chr1:171050404-171050731	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr1:171050520-171050670	MCF-7	breast:	n/a	n/a
43	CTCF	chr1:171050480-171050630	GM06990	blood:	n/a	n/a
44	SMC3	chr1:171050446-171050785	HepG2	liver:	n/a	n/a
45	RAD21	chr1:171050303-171050949	HCT-116	colon:	n/a	n/a
46	CTCF	chr1:171050480-171050630	BJ	skin:	n/a	n/a
47	CTCF	chr1:171050480-171050630	HCT-116	colon:	n/a	n/a
48	CTCF	chr1:171050460-171050610	HCPEpiC	choroid plexus:	n/a	n/a
49	CTCF	chr1:171050383-171050761	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr1:171050476-171050672	Kidney_OC	kidney:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:171049785..171051089-chr1:171157506..171158409,9	MCF-7	breast:
2	chr1:171050091..171050825-chr1:171157560..171158443,3	MCF-7	breast:
3	chr1:171050144..171051119-chr1:171195616..171196435,6	MCF-7	breast:
4	chr1:171050311..171050975-chr1:171195652..171196489,2	MCF-7	breast:
5	chr1:171050389..171052635-chr1:171054264..171056388,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000226552	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12402693	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs12404183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12404218	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16863989	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16863990	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs28363515	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28745581	0.86[ASN][1000 genomes]
rs28745584	0.86[ASN][1000 genomes]
rs3754489	0.82[CHB][hapmap];1.00[ASN][1000 genomes]
rs3754491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66937021	1.00[ASN][1000 genomes]
rs67806272	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67975878	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7051095	0.89[AFR][1000 genomes]
rs7053972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7057100	0.85[EUR][1000 genomes]
rs7066402	0.85[EUR][1000 genomes]
rs72637246	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72712638	0.95[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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171050000-171050800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:171050000-171051000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr1:171050000-171051000	Enhancers	Brain Germinal Matrix	brain
4	chr1:171050200-171053800	Enhancers	Fetal Intestine Large	intestine
5	chr1:171050400-171051400	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links