Variant report

Variant	rs4971087
Chromosome Location	chr1:155562065-155562066
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	CTCF	chr1:155561526-155562219	SK-N-SH	brain:	n/a	chr1:155561779-155561792 chr1:155561777-155561795 chr1:155561778-155561794 chr1:155561772-155561793
2	CTCF	chr1:155561920-155562070	GM12870	blood:	n/a	n/a
3	SMC3	chr1:155561523-155562357	SK-N-SH	brain:	n/a	chr1:155561779-155561793
4	RAD21	chr1:155561575-155562220	SK-N-SH	brain:	n/a	chr1:155561775-155561794 chr1:155561779-155561793
5	USF1	chr1:155562059-155562354	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155290471..155293068-chr1:155560702..155562665,2	MCF-7	breast:
2	chr1:155220501..155221072-chr1:155561223..155562223,2	K562	blood:
3	chr1:155561838..155563770-chr1:155565772..155568084,2	K562	blood:

Variant related genes	Relation type
ENSG00000223503	TF binding region
ENSG00000160753	Chromatin interaction
ENSG00000225855	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10752610	1.00[ASN][1000 genomes]
rs10908468	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1094462	0.82[EUR][1000 genomes]
rs11803678	0.82[EUR][1000 genomes]
rs12077729	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13374129	0.82[EUR][1000 genomes]
rs1624846	0.82[EUR][1000 genomes]
rs16837037	0.82[EUR][1000 genomes]
rs171167	0.92[EUR][1000 genomes]
rs17367421	1.00[ASN][1000 genomes]
rs17377506	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1749421	0.82[EUR][1000 genomes]
rs1765284	0.80[EUR][1000 genomes]
rs1962247	0.87[EUR][1000 genomes]
rs2477541	0.82[EUR][1000 genomes]
rs2686255	0.82[EUR][1000 genomes]
rs28574887	0.82[EUR][1000 genomes]
rs348206	0.92[EUR][1000 genomes]
rs35044707	0.82[EUR][1000 genomes]
rs41264969	0.87[EUR][1000 genomes]
rs4612618	0.82[EUR][1000 genomes]
rs4933	0.87[EUR][1000 genomes]
rs4971050	1.00[ASN][1000 genomes]
rs4971086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs543854	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548809	0.87[EUR][1000 genomes]
rs552778	0.87[EUR][1000 genomes]
rs56758819	0.82[EUR][1000 genomes]
rs59706606	0.82[EUR][1000 genomes]
rs59791187	0.82[EUR][1000 genomes]
rs61258690	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621181	0.87[EUR][1000 genomes]
rs682020	0.82[EUR][1000 genomes]
rs73001021	0.82[EUR][1000 genomes]
rs7340058	1.00[ASN][1000 genomes]
rs7525057	0.92[EUR][1000 genomes]
rs7535158	0.92[EUR][1000 genomes]
rs822016	0.82[EUR][1000 genomes]
rs822018	0.82[EUR][1000 genomes]
rs822019	0.82[EUR][1000 genomes]
rs822020	0.82[EUR][1000 genomes]
rs822022	0.82[EUR][1000 genomes]
rs9426929	0.87[EUR][1000 genomes]
rs9427223	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv3431739	chr1:155514331-155664183	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	esv3388968	chr1:155532335-155658278	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats 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	55 gene(s)	inside rSNPs	diseases
5	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv436522	chr1:155559513-155674249	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv946419	chr1:155561148-155630744	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155534600-155565800	Weak transcription	Brain Hippocampus Middle	brain
2	chr1:155534800-155565600	Weak transcription	Brain Angular Gyrus	brain
3	chr1:155534800-155568400	Weak transcription	Thymus	Thymus
4	chr1:155535000-155570400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:155535400-155564000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:155540400-155565800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:155541400-155569000	Weak transcription	HSMMtube	muscle
8	chr1:155541600-155565600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:155541600-155565600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:155541600-155568400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:155542000-155565600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:155542200-155562800	Weak transcription	Fetal Muscle Leg	muscle
13	chr1:155554000-155566400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:155557200-155568600	Weak transcription	NHEK	skin
15	chr1:155558400-155568600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:155559000-155568800	Weak transcription	HSMM	muscle
17	chr1:155559200-155565600	Weak transcription	Fetal Brain Female	brain
18	chr1:155560400-155562200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:155560600-155565800	Weak transcription	Brain Anterior Caudate	brain
20	chr1:155560600-155568400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:155560600-155568400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:155560600-155570400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:155561000-155568800	Weak transcription	Lung	lung
24	chr1:155561200-155568400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:155561200-155568600	Weak transcription	Fetal Stomach	stomach
26	chr1:155561400-155568200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:155561800-155562200	Enhancers	Brain Cingulate Gyrus	brain
28	chr1:155561800-155562200	Enhancers	Hela-S3	cervix
29	chr1:155562000-155564200	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links