Variant report

Variant	rs11702158
Chromosome Location	chr21:40498268-40498269
allele	C/T
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	RAD21	chr21:40497758-40498292	A549	lung:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
2	RAD21	chr21:40497650-40498387	ECC-1	luminal epithelium:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
3	CEBPB	chr21:40497807-40498325	MCF-7	breast:	n/a	chr21:40498084-40498095
4	RAD21	chr21:40497802-40498367	HCT-116	colon:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
5	CTCF	chr21:40498240-40498390	K562	blood:	n/a	n/a
6	CEBPB	chr21:40497837-40498337	MCF-7	breast:	n/a	chr21:40498084-40498095
7	RAD21	chr21:40497257-40498635	SK-N-SH	brain:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
8	RAD21	chr21:40497707-40498304	IMR90	lung:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
9	CTCF	chr21:40498260-40498410	GM06990	blood:	n/a	n/a
10	MAX	chr21:40497456-40498317	MCF-7	breast:	n/a	n/a
11	RAD21	chr21:40497588-40498327	H1-hESC	embryonic stem cell:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
12	CTCF	chr21:40497726-40498305	A549	lung:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
13	CTCF	chr21:40497829-40498292	IMR90	lung:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
14	CTCF	chr21:40497622-40498606	SK-N-SH	brain:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
15	SMC3	chr21:40497671-40498342	HepG2	liver:	n/a	chr21:40498057-40498071
16	RAD21	chr21:40497694-40498316	SK-N-SH_RA	brain:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
17	RAD21	chr21:40497656-40498437	MCF-7	breast:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
18	CTCF	chr21:40497844-40498310	K562	blood:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
19	CTCF	chr21:40497825-40498366	MCF-7	breast:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
20	RAD21	chr21:40497828-40498280	HepG2	liver:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
21	CEBPB	chr21:40497927-40498284	A549	lung:	n/a	chr21:40498084-40498095
22	CTCF	chr21:40497775-40498347	HCT-116	colon:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
23	CTCF	chr21:40498220-40498370	NHEK	skin:	n/a	n/a
24	RAD21	chr21:40497801-40498447	Hela-S3	cervix:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
25	SMC3	chr21:40497459-40498802	SK-N-SH	brain:	n/a	chr21:40498057-40498071
26	RAD21	chr21:40497671-40498382	HCT-116	colon:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
27	CTCF	chr21:40497744-40498331	MCF-7	breast:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
28	RAD21	chr21:40497735-40498384	MCF-7	breast:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
29	RAD21	chr21:40497782-40498300	ECC-1	luminal epithelium:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
30	CTCF	chr21:40498240-40498390	HRPEpiC	eye:	n/a	n/a
31	RAD21	chr21:40497686-40498292	H1-hESC	embryonic stem cell:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126

No.	Distal block	Cell Line	Cell type
1	chr21:40105498..40106623-chr21:40497124..40499103,7	MCF-7	breast:
2	chr21:40480387..40482431-chr21:40496618..40498616,2	MCF-7	breast:
3	chr21:40460586..40461779-chr21:40497559..40498490,3	MCF-7	breast:
4	chr21:40493420..40495416-chr21:40496679..40498868,2	K562	blood:
5	chr21:40176646..40177691-chr21:40497667..40498470,3	MCF-7	breast:
6	chr21:40468353..40468958-chr21:40497933..40498489,3	MCF-7	breast:
7	chr21:40488161..40490338-chr21:40496446..40499117,2	K562	blood:
8	chr21:40496928..40499014-chr21:40502516..40504228,2	K562	blood:
9	chr21:40176334..40177511-chr21:40497580..40498463,5	MCF-7	breast:

Variant related genes	Relation type
RPL23AP12	TF binding region
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11702077	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242948	0.83[ASN][1000 genomes]
rs2836894	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836896	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836899	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836903	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836904	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836905	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836906	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836908	0.84[ASN][1000 genomes]
rs2836909	0.82[ASN][1000 genomes]
rs2836911	0.82[ASN][1000 genomes]
rs2836918	0.83[CHB][hapmap]
rs34912726	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34989336	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4817990	0.94[ASN][1000 genomes]
rs56147949	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62224879	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7510385	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8131292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8131570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11702158	HMGN1	cis	multi-tissue	Pritchard
rs11702158	BRWD1	cis	multi-tissue	Pritchard
rs11702158	BRWD1	cis	Lymphoblastoid	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40496000-40498400	Enhancers	Dnd41	blood
2	chr21:40496200-40498400	Enhancers	Fetal Muscle Leg	muscle
3	chr21:40496200-40498400	Enhancers	NHDF-Ad	bronchial
4	chr21:40496200-40498600	Enhancers	HepG2	liver
5	chr21:40496200-40498800	Enhancers	Fetal Stomach	stomach
6	chr21:40496400-40498400	Enhancers	Fetal Lung	lung
7	chr21:40496400-40498800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr21:40496800-40498400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr21:40497000-40498400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr21:40497000-40498800	Enhancers	Lung	lung
11	chr21:40497400-40498400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr21:40497400-40498600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr21:40497600-40498400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr21:40497600-40498400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr21:40497800-40498800	Enhancers	Fetal Muscle Trunk	muscle
16	chr21:40497800-40506200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr21:40498000-40499200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr21:40498000-40500200	Weak transcription	Right Atrium	heart
19	chr21:40498000-40503000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr21:40498000-40503000	Weak transcription	Esophagus	oesophagus
21	chr21:40498000-40503200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr21:40498000-40503200	Weak transcription	Psoas Muscle	Psoas

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