Variant report

Variant	rs1981412
Chromosome Location	chr11:71138710-71138711
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:71138540..71142714-chr11:71144455..71147360,4	K562	blood:
2	chr11:71137647..71140040-chr11:71141812..71145984,4	K562	blood:
3	chr11:71130483..71134539-chr11:71135016..71139274,7	MCF-7	breast:
4	chr11:71137158..71140424-chr11:71155885..71157748,3	K562	blood:

Variant related genes	Relation type
ENSG00000172900	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1044482	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11233746	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11233747	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11233789	0.81[EUR][1000 genomes]
rs11546509	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11600569	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11600860	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11603330	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11604642	0.84[ASN][1000 genomes]
rs11606033	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11606612	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11606631	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12278461	0.81[EUR][1000 genomes]
rs12419279	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12419334	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12422045	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12785878	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12789751	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12790010	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12790558	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12791871	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12792306	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12793224	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12793530	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12794668	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12797951	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12800438	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12803256	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12806844	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12807718	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12808368	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1792280	0.81[EUR][1000 genomes]
rs2002063	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2040323	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2276360	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276361	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2276362	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2282620	0.81[EUR][1000 genomes]
rs2282621	0.81[EUR][1000 genomes]
rs28364617	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2852853	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3750997	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3794060	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4423214	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4488226	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944044	0.84[ASN][1000 genomes]
rs4944062	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4944946	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4944949	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4944955	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944956	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944958	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4944959	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4945008	0.84[ASN][1000 genomes]
rs732934	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7928249	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7935125	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7938885	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7944926	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs909217	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1981412	NADSYN1	cis	Nerve Tibial	GTEx
rs1981412	RP11-660L16.2	cis	Thyroid	GTEx
rs1981412	RP11-660L16.2	cis	Nerve Tibial	GTEx
rs1981412	NADSYN1	cis	Thyroid	GTEx
rs1981412	RP11-660L16.2	cis	Adipose Subcutaneous	GTEx
rs1981412	RP11-660L16.2	cis	Esophagus Muscularis	GTEx
rs1981412	RP11-660L16.2	cis	Whole Blood	GTEx
rs1981412	RP11-660L16.2	cis	Muscle Skeletal	GTEx
rs1981412	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71123600-71139600	Weak transcription	Right Atrium	heart
2	chr11:71132600-71144000	Weak transcription	Spleen	Spleen
3	chr11:71135000-71150600	Weak transcription	NH-A	brain
4	chr11:71135400-71139600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr11:71135400-71145000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:71137000-71140000	Weak transcription	Stomach Mucosa	stomach
7	chr11:71137000-71144800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:71137200-71140200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:71137200-71144000	Weak transcription	Hela-S3	cervix
10	chr11:71137200-71145000	Weak transcription	Brain Germinal Matrix	brain
11	chr11:71137200-71149600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr11:71137600-71146000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:71137800-71138800	Weak transcription	GM12878-XiMat	blood
14	chr11:71137800-71139600	Weak transcription	Adipose Nuclei	Adipose
15	chr11:71137800-71140000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:71138000-71139400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:71138000-71144800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:71138000-71145200	Weak transcription	HMEC	breast

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