Variant report

Variant	rs1790373
Chromosome Location	chr11:71166337-71166338
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:71162324..71166430-chr11:71186520..71190924,4	K562	blood:

Variant related genes	Relation type
ENSG00000172890	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1044535	0.94[EUR][1000 genomes]
rs10751102	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10792743	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10898117	0.94[EUR][1000 genomes]
rs11233555	0.82[CHB][hapmap]
rs11233606	0.94[EUR][1000 genomes]
rs11608138	1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12281481	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1623080	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1626291	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1790325	0.94[EUR][1000 genomes]
rs1790326	0.94[EUR][1000 genomes]
rs1790327	0.94[EUR][1000 genomes]
rs1790329	0.94[EUR][1000 genomes]
rs1790334	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790337	0.84[EUR][1000 genomes]
rs1790346	1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1790347	0.94[EUR][1000 genomes]
rs1790348	0.94[EUR][1000 genomes]
rs1790351	1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1790354	0.94[EUR][1000 genomes]
rs1790355	0.94[EUR][1000 genomes]
rs1790356	0.89[EUR][1000 genomes]
rs1790357	0.94[EUR][1000 genomes]
rs1792265	0.94[EUR][1000 genomes]
rs1792268	0.94[EUR][1000 genomes]
rs1792270	0.94[EUR][1000 genomes]
rs1792271	0.94[EUR][1000 genomes]
rs1792272	0.94[EUR][1000 genomes]
rs1792273	1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs1792274	0.94[EUR][1000 genomes]
rs1792275	0.94[EUR][1000 genomes]
rs1792276	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1792279	0.97[EUR][1000 genomes]
rs1792285	0.94[EUR][1000 genomes]
rs1792316	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792319	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2002906	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2155425	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2186773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2186778	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276353	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282617	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282618	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282619	1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298772	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2511279	0.82[EUR][1000 genomes]
rs2851693	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763859	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763860	0.81[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3794065	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3794066	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3794067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3814731	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3814734	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944075	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944080	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944997	1.00[CEU][hapmap]
rs4944999	0.88[ASN][1000 genomes]
rs4945001	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4945007	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4945013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6592154	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6592180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7110053	0.94[EUR][1000 genomes]
rs7110316	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7113783	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7123973	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7124675	0.94[EUR][1000 genomes]
rs7129099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs751389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs760241	0.94[EUR][1000 genomes]
rs7690	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7926054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7950584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs949176	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs949177	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs949178	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1037357	chr11:71162241-71209628	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
8	nsv541085	chr11:71162241-71209628	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1790373	NADSYN1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71165000-71210000	Weak transcription	Psoas Muscle	Psoas
2	chr11:71165200-71166400	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr11:71165200-71166600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr11:71165200-71169800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:71165200-71169800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:71165200-71177400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:71165200-71177600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr11:71165200-71199200	Weak transcription	Right Atrium	heart
9	chr11:71165400-71166400	Enhancers	Colonic Mucosa	Colon
10	chr11:71165400-71166600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:71165400-71166600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:71165400-71170000	Weak transcription	Small Intestine	intestine
13	chr11:71165400-71194200	Weak transcription	Fetal Heart	heart
14	chr11:71165600-71166600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr11:71165800-71166400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr11:71165800-71167000	Weak transcription	NH-A	brain
17	chr11:71165800-71167200	Genic enhancers	Dnd41	blood
18	chr11:71165800-71168200	Strong transcription	Hela-S3	cervix
19	chr11:71165800-71168600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:71165800-71168800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr11:71165800-71169400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:71165800-71170000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:71165800-71171200	Strong transcription	K562	blood
24	chr11:71165800-71171800	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr11:71165800-71172400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:71165800-71173000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr11:71165800-71174000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:71165800-71175800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr11:71165800-71178200	Strong transcription	NHLF	lung
30	chr11:71165800-71178400	Strong transcription	Fetal Stomach	stomach
31	chr11:71165800-71179200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:71165800-71179200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:71165800-71179200	Strong transcription	Fetal Muscle Leg	muscle
34	chr11:71165800-71180400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr11:71165800-71218400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr11:71166000-71166400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr11:71166000-71166400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr11:71166000-71166400	Genic enhancers	Fetal Intestine Large	intestine
39	chr11:71166000-71166600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:71166000-71166800	Genic enhancers	GM12878-XiMat	blood
41	chr11:71166000-71168000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr11:71166000-71169400	Strong transcription	NHEK	skin
43	chr11:71166000-71169600	Strong transcription	Placenta	Placenta
44	chr11:71166000-71171400	Strong transcription	Brain Angular Gyrus	brain
45	chr11:71166000-71171600	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr11:71166000-71171600	Strong transcription	Brain Germinal Matrix	brain
47	chr11:71166000-71172000	Strong transcription	Fetal Brain Female	brain
48	chr11:71166000-71173000	Strong transcription	Osteobl	bone
49	chr11:71166000-71173600	Strong transcription	HSMM	muscle
50	chr11:71166000-71173800	Strong transcription	Brain Substantia Nigra	brain

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