Variant report

Variant	rs1790345
Chromosome Location	chr11:71145941-71145942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:71137647..71140040-chr11:71141812..71145984,4	K562	blood:
2	chr11:71144482..71146798-chr11:71158407..71160975,3	K562	blood:
3	chr11:71145861..71148478-chr11:71150680..71152334,2	K562	blood:
4	chr11:71138540..71142714-chr11:71144455..71147360,4	K562	blood:
5	chr11:71144398..71146962-chr11:71155881..71158329,2	K562	blood:

Variant related genes	Relation type
ENSG00000254682	Chromatin interaction
ENSG00000172893	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10898144	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1123007	0.84[ASN][1000 genomes]
rs11603330	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs11606033	0.81[CEU][hapmap]
rs12224205	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12419279	1.00[CEU][hapmap]
rs12419334	0.84[TSI][hapmap]
rs12422045	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs12797951	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs1540127	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1619577	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1629220	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1630498	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790324	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790328	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790330	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790339	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1790340	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1790341	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1790343	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1790344	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1790350	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790353	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792224	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1792226	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1792227	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1792229	0.94[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1792231	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1792233	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1792234	0.94[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1792235	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1792264	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1792277	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792280	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792281	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792282	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792283	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1792284	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792315	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1894100	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2002064	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2017686	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2276358	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2276362	0.80[CEU][hapmap]
rs2282621	0.82[TSI][hapmap]
rs2511010	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3750997	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs3794057	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4402322	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4435028	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4616066	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4944957	0.82[TSI][hapmap]
rs736894	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7928249	0.82[TSI][hapmap]
rs7935125	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
7	nsv518163	chr11:71142350-71155153	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1790345	RAB6A	cis	cerebellum	SCAN
rs1790345	RP11-660L16.2	cis	Thyroid	GTEx
rs1790345	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs1790345	AIP	cis	parietal	SCAN
rs1790345	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs1790345	NADSYN1	cis	lymphoblastoid	seeQTL
rs1790345	NADSYN1	cis	Nerve Tibial	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71135000-71150600	Weak transcription	NH-A	brain
2	chr11:71137200-71149600	Weak transcription	Primary B cells from peripheral blood	blood
3	chr11:71137600-71146000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr11:71140600-71158200	Weak transcription	Fetal Brain Male	brain
5	chr11:71140800-71154000	Weak transcription	Fetal Lung	lung
6	chr11:71140800-71154000	Weak transcription	HSMM	muscle
7	chr11:71141200-71148200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:71142400-71146800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr11:71142600-71146000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:71142600-71146000	Weak transcription	Thymus	Thymus
11	chr11:71142800-71147800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:71143000-71148200	Weak transcription	NHDF-Ad	bronchial
13	chr11:71143000-71148400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr11:71143000-71150600	Weak transcription	Osteobl	bone
15	chr11:71143600-71146000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:71143600-71146400	Weak transcription	Aorta	Aorta
17	chr11:71143600-71149400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr11:71143800-71146400	Enhancers	Placenta	Placenta
19	chr11:71144000-71146200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr11:71144000-71147000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:71144000-71156200	Strong transcription	Fetal Brain Female	brain
22	chr11:71144200-71146000	Weak transcription	Dnd41	blood
23	chr11:71144200-71146400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr11:71144200-71147000	Genic enhancers	Spleen	Spleen
25	chr11:71144200-71152000	Weak transcription	Fetal Thymus	thymus
26	chr11:71144200-71158200	Weak transcription	Small Intestine	intestine
27	chr11:71144400-71146200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr11:71144400-71156200	Strong transcription	Primary T cells from cord blood	blood
29	chr11:71144600-71148000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr11:71144600-71148400	Weak transcription	Pancreas	Pancrea
31	chr11:71144600-71157800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr11:71144800-71146200	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:71144800-71147200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:71144800-71147200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:71144800-71149400	Weak transcription	Primary B cells from cord blood	blood
36	chr11:71144800-71156600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:71144800-71156800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:71144800-71156800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:71144800-71157800	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr11:71145000-71146000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:71145000-71146000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:71145000-71146000	Genic enhancers	Fetal Muscle Leg	muscle
43	chr11:71145000-71146200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:71145000-71146200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr11:71145000-71146800	Strong transcription	GM12878-XiMat	blood
46	chr11:71145000-71147000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:71145000-71147000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr11:71145000-71147600	Strong transcription	NHEK	skin
49	chr11:71145000-71148000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr11:71145000-71148800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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