Variant report

Variant	rs3782661
Chromosome Location	chr12:21659121-21659122
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	REST	chr12:21658767-21659274	ECC-1	luminal epithelium:	n/a	n/a
2	REST	chr12:21658779-21659205	HL-60	blood:	n/a	n/a
3	REST	chr12:21658812-21659155	Hela-S3	cervix:	n/a	n/a
4	REST	chr12:21658834-21659277	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:21657807..21659744-chr12:21755887..21758843,2	MCF-7	breast:
2	chr12:21655984..21659478-chr12:21666041..21668591,3	K562	blood:
3	chr12:21647474..21650323-chr12:21658442..21660780,2	K562	blood:

Variant related genes	Relation type
RECQL	TF binding region
ENSG00000111713	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10492117	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10770819	0.81[CEU][hapmap];0.84[CHB][hapmap];0.81[EUR][1000 genomes]
rs10841835	0.93[CEU][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10841836	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10841837	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10841839	0.85[CHB][hapmap]
rs10841840	0.85[CHB][hapmap]
rs11046089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11046093	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs11046098	0.85[CHB][hapmap]
rs12582513	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs12582514	0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs12822436	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2110159	0.92[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2284394	0.84[JPT][hapmap]
rs2284395	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2300211	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2300212	0.82[ASN][1000 genomes]
rs2417991	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34965831	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35538394	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4762834	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4762835	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61926331	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised 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	27 gene(s)	inside rSNPs	diseases
2	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1054220	chr12:21612158-21692103	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1036084	chr12:21631009-21792756	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3782661	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs3782661	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs3782661	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs3782661	LOC642732	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21655400-21674800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:21655600-21659400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:21655600-21660800	Weak transcription	Left Ventricle	heart
4	chr12:21655600-21661800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:21655600-21666000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:21656000-21659400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:21656000-21660000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:21656000-21660400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:21656000-21660800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:21656000-21660800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:21656000-21661000	Weak transcription	Fetal Intestine Large	intestine
12	chr12:21656000-21671800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:21656000-21672800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:21656000-21674000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:21656000-21674600	Weak transcription	Fetal Kidney	kidney
16	chr12:21656200-21660000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr12:21656200-21660000	Weak transcription	Placenta	Placenta
18	chr12:21656200-21660200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:21656200-21660600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:21656200-21660800	Weak transcription	Primary B cells from cord blood	blood
21	chr12:21656200-21660800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr12:21656200-21660800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr12:21656200-21660800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:21656200-21662000	Weak transcription	Fetal Intestine Small	intestine
25	chr12:21656200-21662000	Weak transcription	Fetal Stomach	stomach
26	chr12:21656200-21662200	Weak transcription	HSMM	muscle
27	chr12:21656200-21664000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:21656200-21665000	Weak transcription	HSMMtube	muscle
29	chr12:21656200-21665200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr12:21656200-21665600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr12:21656200-21666200	Weak transcription	Colonic Mucosa	Colon
32	chr12:21656200-21669800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:21656200-21671800	Weak transcription	Thymus	Thymus
34	chr12:21656200-21680000	Weak transcription	Right Ventricle	heart
35	chr12:21656400-21659200	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr12:21656400-21660600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:21656400-21660600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:21656400-21660800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr12:21656400-21661000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr12:21656400-21662600	Weak transcription	Brain Germinal Matrix	brain
41	chr12:21656400-21668000	Weak transcription	Fetal Lung	lung
42	chr12:21656400-21680200	Weak transcription	Aorta	Aorta
43	chr12:21656600-21660600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr12:21656600-21663800	Weak transcription	NHLF	lung
45	chr12:21656600-21665200	Weak transcription	NHEK	skin
46	chr12:21656600-21665400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr12:21656600-21665800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:21656600-21669200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:21656800-21660000	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr12:21656800-21660400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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