Variant report

Variant	rs10742814
Chromosome Location	chr11:47554337-47554338
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47543706..47547000-chr11:47553093..47555540,3	K562	blood:
2	chr11:47553390..47555536-chr11:47600207..47602219,2	K562	blood:
3	chr11:47553494..47556204-chr11:47558570..47560706,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213619	Chromatin interaction
ENSG00000149187	Chromatin interaction
ENSG00000123444	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1056387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap]
rs10742817	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs10769264	0.95[JPT][hapmap]
rs10769288	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs10838702	0.84[GIH][hapmap]
rs10838709	0.84[GIH][hapmap];0.95[JPT][hapmap]
rs10838725	0.82[ASN][1000 genomes]
rs10838726	0.95[JPT][hapmap]
rs10838732	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs10838740	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs10838746	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs11039225	0.84[GIH][hapmap];0.95[JPT][hapmap]
rs11039244	0.90[JPT][hapmap]
rs11039280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039329	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs11039332	0.89[GIH][hapmap];0.90[JPT][hapmap]
rs11039345	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap]
rs12226590	0.86[AMR][1000 genomes]
rs12285933	1.00[YRI][hapmap]
rs12286721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs12292911	0.84[GIH][hapmap];0.95[JPT][hapmap]
rs12785949	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs1377416	0.84[GIH][hapmap]
rs1534576	0.84[GIH][hapmap]
rs2203712	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2242081	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2290851	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs2293576	0.93[GIH][hapmap];0.95[JPT][hapmap]
rs3740699	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3758655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs4539273	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs4752860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs6485758	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6485763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7103648	0.95[JPT][hapmap]
rs7120548	0.91[GIH][hapmap];0.95[JPT][hapmap]
rs7129797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7933019	0.95[JPT][hapmap]
rs7936948	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs7939420	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs7950696	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10742814	CRY2	cis	parietal	SCAN
rs10742814	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs10742814	MTCH2	cis	cerebellum	SCAN
rs10742814	SLC39A13	cis	cerebellum	SCAN
rs10742814	SLC35C1	cis	parietal	SCAN
rs10742814	C1QTNF4	cis	lymphoblastoid	seeQTL
rs10742814		cis	Lymphoblastoid	GTEx
rs10742814	ATG13	cis	parietal	SCAN
rs10742814	C1QTNF4	cis	multi-tissue	Pritchard
rs10742814	FNBP4	cis	lesional skin	skin_eQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47546000-47572400	Weak transcription	Fetal Intestine Large	intestine
2	chr11:47546200-47560400	Weak transcription	Esophagus	oesophagus
3	chr11:47546400-47558000	Weak transcription	Fetal Lung	lung
4	chr11:47546400-47560400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:47546400-47560800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr11:47546400-47561200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:47546400-47564200	Weak transcription	Thymus	Thymus
8	chr11:47546400-47573400	Weak transcription	Colonic Mucosa	Colon
9	chr11:47546400-47573600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:47546600-47561000	Weak transcription	Stomach Mucosa	stomach
11	chr11:47546800-47559000	Strong transcription	Fetal Intestine Small	intestine
12	chr11:47546800-47560200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr11:47547000-47557800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr11:47547200-47555200	Weak transcription	Primary B cells from cord blood	blood
15	chr11:47547200-47559600	Weak transcription	HUVEC	blood vessel
16	chr11:47547400-47558000	Weak transcription	Small Intestine	intestine
17	chr11:47547400-47560400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr11:47547400-47560800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr11:47547800-47554400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:47547800-47555000	Weak transcription	Right Ventricle	heart
21	chr11:47547800-47562000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:47548200-47560400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr11:47549000-47559400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:47549200-47556400	Weak transcription	Primary T cells from cord blood	blood
25	chr11:47550000-47556400	Weak transcription	A549	lung
26	chr11:47550400-47559200	Weak transcription	NHEK	skin
27	chr11:47550600-47561000	Weak transcription	Placenta	Placenta
28	chr11:47550800-47558000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr11:47551000-47563200	Enhancers	Fetal Brain Male	brain
30	chr11:47551200-47559000	Weak transcription	Psoas Muscle	Psoas
31	chr11:47551400-47554800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:47551400-47555000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr11:47551400-47557600	Weak transcription	Fetal Thymus	thymus
34	chr11:47551800-47555000	Enhancers	Fetal Heart	heart
35	chr11:47551800-47555400	Enhancers	Brain Anterior Caudate	brain
36	chr11:47552000-47554800	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr11:47552000-47555600	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr11:47552200-47554400	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr11:47552200-47555600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr11:47552200-47556000	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr11:47552200-47560400	Weak transcription	HMEC	breast
42	chr11:47552400-47555000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr11:47552400-47556800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr11:47552600-47555800	Enhancers	Liver	Liver
45	chr11:47552600-47560800	Weak transcription	Pancreas	Pancrea
46	chr11:47553000-47554600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr11:47553000-47555400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr11:47553000-47556800	Weak transcription	Lung	lung
49	chr11:47553000-47557800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:47553000-47557800	Weak transcription	Spleen	Spleen

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