Variant report

Variant	rs4542420
Chromosome Location	chr11:66277610-66277611
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr11:66277571-66278254	K562	blood:	n/a	n/a
2	TAF1	chr11:66277604-66278520	H1-neurons	neurons:	n/a	n/a
3	REST	chr11:66277566-66278743	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr11:66277595-66278429	K562	blood:	n/a	n/a
5	POLR2A	chr11:66277394-66277610	HepG2	liver:	n/a	n/a
6	MAZ	chr11:66277478-66278377	IMR90	lung:	n/a	chr11:66278094-66278104
7	POLR2A	chr11:66277568-66278661	H1-hESC	embryonic stem cell:	n/a	n/a
8	MXI1	chr11:66277457-66278887	SK-N-SH	brain:	n/a	chr11:66278105-66278120 chr11:66278107-66278122
9	POLR2A	chr11:66277601-66278284	K562	blood:	n/a	n/a
10	POLR2A	chr11:66277581-66278458	PFSK-1	brain:	n/a	n/a
11	HCFC1	chr11:66277454-66278913	Hela-S3	cervix:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66240065..66243058-chr11:66275897..66279906,3	MCF-7	breast:
2	chr11:66277230..66279524-chr11:66443471..66447477,3	K562	blood:
3	chr11:66276194..66279522-chr11:66281470..66284393,4	MCF-7	breast:
4	chr11:66277351..66279482-chr11:66383310..66385762,3	K562	blood:
5	chr11:66275530..66280458-chr11:66280685..66284919,6	K562	blood:
6	chr11:66244850..66249884-chr11:66274125..66278778,6	MCF-7	breast:
7	chr11:66277334..66280308-chr11:66282116..66284343,2	MCF-7	breast:
8	chr11:66277255..66279154-chr11:66443896..66445716,2	MCF-7	breast:
9	chr11:66277249..66279573-chr11:66442892..66445928,3	K562	blood:
10	chr11:66234037..66235984-chr11:66277120..66279562,2	MCF-7	breast:

No data

Variant related genes	Relation type
BBS1	TF binding region
ENSG00000248643	Chromatin interaction
ENSG00000174516	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000173914	Chromatin interaction
ENSG00000174547	Chromatin interaction
ENSG00000255517	Chromatin interaction
ENSG00000254986	Chromatin interaction
ENSG00000174483	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10501397	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896124	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896125	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896129	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11227495	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227497	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227498	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227499	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227501	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227502	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227506	0.86[ASN][1000 genomes]
rs11227509	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227510	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227511	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227512	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227514	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227515	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227522	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11227523	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227525	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11227527	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11227534	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11550299	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11821155	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11822028	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11822099	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11824771	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12099041	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12221821	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12223479	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12272545	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17065	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17147644	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17495838	0.82[EUR][1000 genomes]
rs17496250	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17496586	0.95[EUR][1000 genomes]
rs17580784	0.87[EUR][1000 genomes]
rs2075792	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2276406	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2277302	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279864	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2279865	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2298806	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305532	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305533	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305534	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305535	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28414721	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3179961	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35733139	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3737525	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3741360	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816492	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3819247	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825065	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3892818	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4576	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4630309	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4930182	0.87[EUR][1000 genomes]
rs4930183	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4930377	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4930378	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4930379	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4930380	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56144989	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57045447	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57207756	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57288351	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57596493	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57634456	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57691879	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57724777	0.93[EUR][1000 genomes]
rs59829960	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59982644	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60358007	0.91[EUR][1000 genomes]
rs60645853	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61561111	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61582507	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7104378	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7116921	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7116940	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7123176	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7928882	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7939759	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7943327	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7950407	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7950790	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv832193	chr11:66120339-66278805	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv468601	chr11:66234023-66296114	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv555224	chr11:66234023-66296114	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4542420	CTD-3074O7.5	cis	Whole Blood	GTEx
rs4542420	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs4542420	DPP3	cis	Thyroid	GTEx
rs4542420	CTD-3074O7.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66248600-66278000	Weak transcription	NHDF-Ad	bronchial
2	chr11:66255800-66277800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr11:66261000-66277800	Weak transcription	Psoas Muscle	Psoas
4	chr11:66261200-66277800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:66261200-66278000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:66261800-66277800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:66263600-66277800	Weak transcription	NH-A	brain
8	chr11:66264600-66278000	Weak transcription	HMEC	breast
9	chr11:66264800-66277800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:66264800-66277800	Weak transcription	Osteobl	bone
11	chr11:66265000-66277800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr11:66265200-66277800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:66266600-66278000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:66272800-66277800	Weak transcription	Aorta	Aorta
15	chr11:66272800-66278000	Weak transcription	Lung	lung
16	chr11:66272800-66278000	Weak transcription	NHLF	lung
17	chr11:66273000-66277800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr11:66273000-66277800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr11:66273000-66277800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:66273000-66277800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr11:66273000-66277800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr11:66273000-66277800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr11:66273000-66277800	Weak transcription	Colonic Mucosa	Colon
24	chr11:66273000-66277800	Weak transcription	Left Ventricle	heart
25	chr11:66273000-66277800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr11:66273000-66277800	Weak transcription	Right Ventricle	heart
27	chr11:66273000-66277800	Weak transcription	HUVEC	blood vessel
28	chr11:66273000-66278000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:66273200-66277800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:66273200-66277800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:66273200-66277800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr11:66273200-66277800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:66273200-66277800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr11:66273200-66277800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:66273200-66277800	Weak transcription	Esophagus	oesophagus
36	chr11:66273200-66277800	Weak transcription	Fetal Brain Female	brain
37	chr11:66273200-66277800	Weak transcription	GM12878-XiMat	blood
38	chr11:66273200-66278000	Weak transcription	Gastric	stomach
39	chr11:66274400-66277800	Weak transcription	Adipose Nuclei	Adipose
40	chr11:66274600-66277800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:66274600-66277800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr11:66274600-66277800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:66274600-66277800	Weak transcription	HSMM	muscle
44	chr11:66276000-66277800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr11:66276000-66277800	Weak transcription	HSMMtube	muscle
46	chr11:66276200-66277800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr11:66276400-66277800	Enhancers	Fetal Heart	heart
48	chr11:66276800-66277800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr11:66277000-66277800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:66277000-66277800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links