Variant report

Variant	rs3781870
Chromosome Location	chr11:107976450-107976451
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:107960048..107962789-chr11:107975595..107977973,2	MCF-7	breast:
2	chr11:107974288..107976486-chr11:107982960..107986332,3	K562	blood:
3	chr11:107974563..107976486-chr11:107983506..107986332,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11212474	0.80[EUR][1000 genomes]
rs11602683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11603079	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11605419	0.80[EUR][1000 genomes]
rs11605878	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11606820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11822270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11822609	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11822651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11825746	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11825936	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11828176	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17107675	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17617000	0.91[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2235000	0.84[YRI][hapmap]
rs3741053	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4565865	0.80[EUR][1000 genomes]
rs58243661	0.82[EUR][1000 genomes]
rs6588998	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7103534	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7107097	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7118335	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs7125285	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs73555391	0.80[EUR][1000 genomes]
rs73557106	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73557111	0.82[EUR][1000 genomes]
rs73557122	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73557155	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73557188	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7927717	0.82[EUR][1000 genomes]
rs7936826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7943669	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7947408	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv3372573	chr11:107880365-108022895	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1039549	chr11:107950572-108034548	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1040522	chr11:107969357-108049672	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3781870	ACAT1	cis	cerebellum	SCAN
rs3781870	ACAT1	cis	parietal	SCAN
rs3781870	GRIA4	cis	parietal	SCAN
rs3781870	GUCY1A2	cis	parietal	SCAN
rs3781870	ACAT1	Cis_1M	lymphoblastoid	RTeQTL
rs3781870	LAYN	cis	parietal	SCAN
rs3781870	MGC33948	cis	multi-tissue	Pritchard
rs3781870	SIK2	cis	parietal	SCAN
rs3781870	NPAT	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107908400-107980600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:107928200-107985200	Weak transcription	Psoas Muscle	Psoas
3	chr11:107946600-107986000	Weak transcription	Brain Angular Gyrus	brain
4	chr11:107953200-107991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr11:107953600-107986000	Weak transcription	Pancreas	Pancrea
6	chr11:107955800-107991800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:107958400-107977200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:107958600-107978200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr11:107958800-107980400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:107959000-107976600	Strong transcription	Fetal Thymus	thymus
11	chr11:107959000-107977000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr11:107959200-107977000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:107959200-107977800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:107960000-107977000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr11:107961400-107977800	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr11:107961600-107976800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr11:107962200-107977000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:107962800-107977600	Weak transcription	Esophagus	oesophagus
19	chr11:107964000-107976800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:107964000-107977200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr11:107964000-107978600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:107964600-107978000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:107965400-107977200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr11:107965600-107976800	Strong transcription	Liver	Liver
25	chr11:107965800-107977200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:107966200-107982200	Weak transcription	Spleen	Spleen
27	chr11:107966200-107986000	Weak transcription	Brain Substantia Nigra	brain
28	chr11:107966400-107992000	Weak transcription	Fetal Brain Male	brain
29	chr11:107966600-107986000	Weak transcription	HMEC	breast
30	chr11:107967000-107991400	Weak transcription	A549	lung
31	chr11:107968200-107986000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr11:107968200-107986800	Weak transcription	Colonic Mucosa	Colon
33	chr11:107968200-107992000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr11:107968600-107978000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr11:107968600-107986000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr11:107969000-107991600	Weak transcription	Hela-S3	cervix
37	chr11:107969200-107978200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr11:107969200-107986000	Weak transcription	NHLF	lung
39	chr11:107969200-107986200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr11:107969200-107991800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr11:107970400-107979400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:107970600-107991600	Weak transcription	HepG2	liver
43	chr11:107971600-107977200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:107971800-107976800	Strong transcription	HSMM	muscle
45	chr11:107972200-107986000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr11:107972400-107985000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr11:107972400-107986400	Weak transcription	NHEK	skin
48	chr11:107972400-107991400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr11:107972400-107991600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr11:107972400-107992000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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