Variant report

Variant	rs11954859
Chromosome Location	chr5:60624958-60624959
allele	A/C
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	ZNF263	chr5:60624566-60625410	HEK293-T-REx	kidney:	n/a	chr5:60625020-60625041
2	RCOR1	chr5:60623071-60628252	IMR90	lung:	n/a	n/a
3	CHD1	chr5:60623202-60631624	IMR90	lung:	n/a	chr5:60629730-60629740 chr5:60629024-60629034 chr5:60629683-60629693 chr5:60629116-60629123 chr5:60629352-60629362 chr5:60627826-60627836
4	TAF1	chr5:60624925-60625285	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr5:60624415-60625590	SK-N-MC	brain:	n/a	n/a
6	CEBPB	chr5:60623988-60625096	IMR90	lung:	n/a	chr5:60624202-60624213
7	KAP1	chr5:60624848-60626830	HEK293	kidney:	n/a	n/a
8	POLR2A	chr5:60623868-60631522	IMR90	lung:	n/a	n/a
9	BRCA1	chr5:60624818-60625078	Hela-S3	cervix:	n/a	chr5:60624858-60624865
10	CEBPB	chr5:60624020-60624961	A549	lung:	n/a	chr5:60624202-60624213
11	MAZ	chr5:60623153-60628543	IMR90	lung:	n/a	chr5:60627550-60627560 chr5:60623720-60623729 chr5:60627234-60627243 chr5:60627832-60627842 chr5:60623721-60623730

No.	Distal block	Cell Line	Cell type
1	chr5:60454421..60471345-chr5:60622342..60633215,36	MCF-7	breast:
2	chr5:60454193..60465680-chr5:60622262..60629761,38	MCF-7	breast:
3	chr5:60621987..60625726-chr5:60627235..60630400,4	MCF-7	breast:
4	chr5:60353410..60356120-chr5:60624338..60627119,3	MCF-7	breast:
5	chr5:60623389..60626002-chr5:60627972..60629688,3	K562	blood:
6	chr5:60605123..60607843-chr5:60623875..60626572,3	MCF-7	breast:

Variant related genes	Relation type
ZSWIM6	TF binding region
ENSG00000251279	Chromatin interaction
ENSG00000188725	Chromatin interaction
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10939902	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12188627	0.84[EUR][1000 genomes]
rs13169711	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13170135	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4604142	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4700418	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6449528	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6449529	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7701440	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7709645	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7720894	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7724551	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60616200-60625000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr5:60616400-60625000	Weak transcription	Gastric	stomach
3	chr5:60616800-60625800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:60617000-60626200	Weak transcription	Esophagus	oesophagus
5	chr5:60617400-60625600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr5:60619200-60625600	Weak transcription	Aorta	Aorta
7	chr5:60619400-60626200	Weak transcription	Small Intestine	intestine
8	chr5:60622400-60625200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:60622400-60625600	Enhancers	Osteobl	bone
10	chr5:60622600-60625400	Enhancers	NH-A	brain
11	chr5:60623000-60625200	Enhancers	HUVEC	blood vessel
12	chr5:60623200-60625200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
13	chr5:60623200-60625200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
14	chr5:60623200-60625200	Enhancers	HSMM	muscle
15	chr5:60623200-60625600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr5:60623200-60625600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:60623200-60625800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:60623200-60626000	Enhancers	HMEC	breast
19	chr5:60623400-60625200	Enhancers	A549	lung
20	chr5:60623400-60626000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:60623600-60625000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:60623600-60625000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:60623600-60625200	Enhancers	Hela-S3	cervix
24	chr5:60623600-60625800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:60623600-60626000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr5:60623600-60626000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr5:60623600-60626000	Enhancers	NHEK	skin
28	chr5:60623600-60626200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr5:60623800-60625200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
30	chr5:60623800-60625400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:60623800-60625600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:60623800-60625600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:60623800-60625600	Enhancers	Fetal Intestine Large	intestine
34	chr5:60623800-60625600	Enhancers	Fetal Intestine Small	intestine
35	chr5:60623800-60625800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr5:60623800-60625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr5:60623800-60626200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:60623800-60626400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr5:60624000-60625000	Enhancers	Fetal Lung	lung
40	chr5:60624000-60625200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
41	chr5:60624000-60625200	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr5:60624000-60625400	Enhancers	Duodenum Mucosa	Duodenum
43	chr5:60624000-60625400	Enhancers	Lung	lung
44	chr5:60624000-60625600	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr5:60624000-60626000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:60624200-60625000	Enhancers	Colon Smooth Muscle	Colon
47	chr5:60624200-60625000	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr5:60624200-60625600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr5:60624200-60625800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr5:60624200-60625800	Enhancers	HSMMtube	muscle

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