Variant report

Variant	rs9834166
Chromosome Location	chr3:23964951-23964952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23961452..23965156-chr3:23999587..24004253,5	MCF-7	breast:
2	chr3:23962952..23965260-chr3:25704895..25707086,2	MCF-7	breast:
3	chr3:23961544..23965594-chr3:24039129..24042717,4	K562	blood:
4	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
5	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
6	chr3:23963756..23966294-chr3:24189854..24192332,2	K562	blood:

Variant related genes	Relation type
ENSG00000264219	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000077097	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1133926	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1136155	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11706297	0.97[ASN][1000 genomes]
rs11710647	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710679	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11711073	0.97[ASN][1000 genomes]
rs11711380	0.90[ASN][1000 genomes]
rs11713246	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718625	0.90[ASN][1000 genomes]
rs12497944	1.00[ASN][1000 genomes]
rs13314607	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318927	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13325754	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1397880	0.97[ASN][1000 genomes]
rs1567581	1.00[ASN][1000 genomes]
rs17787211	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2361013	0.97[ASN][1000 genomes]
rs28522849	0.97[ASN][1000 genomes]
rs28623591	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34476593	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35711415	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35886023	0.97[ASN][1000 genomes]
rs4131864	1.00[ASN][1000 genomes]
rs60699428	0.91[ASN][1000 genomes]
rs61294694	0.97[ASN][1000 genomes]
rs61645368	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62253361	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62253380	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62253382	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62253383	0.91[ASN][1000 genomes]
rs62253387	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6550809	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6778970	0.88[EUR][1000 genomes]
rs6787216	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6789983	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6800407	0.92[EUR][1000 genomes]
rs72627066	0.90[EUR][1000 genomes]
rs73825116	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73825124	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73825170	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73825178	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73825181	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629325	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637968	0.84[EUR][1000 genomes]
rs8933	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs938078	0.97[ASN][1000 genomes]
rs9815334	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9836860	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9836970	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9838694	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850255	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9856727	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9857442	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9863605	0.94[ASN][1000 genomes]
rs9863674	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875213	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876561	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9834166	NKIRAS1	Cis_1M	lymphoblastoid	RTeQTL
rs9834166	NR1D2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23959600-23965200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:23959600-23965600	Weak transcription	Spleen	Spleen
3	chr3:23959600-23969400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:23959800-23965000	Weak transcription	Ovary	ovary
5	chr3:23960000-23965000	Weak transcription	Colonic Mucosa	Colon
6	chr3:23960200-23967000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:23960200-23969400	Weak transcription	Esophagus	oesophagus
8	chr3:23960600-23965000	Strong transcription	Fetal Stomach	stomach
9	chr3:23960800-23965000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:23961000-23966600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:23961400-23966000	Strong transcription	Stomach Smooth Muscle	stomach
12	chr3:23961800-23972800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:23961800-23980200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:23962000-23965000	Weak transcription	HSMMtube	muscle
15	chr3:23962000-23965200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:23962000-23965400	Strong transcription	Fetal Brain Female	brain
17	chr3:23962000-23965600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:23962000-23965600	Strong transcription	Colon Smooth Muscle	Colon
19	chr3:23962000-23968200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr3:23962000-23968400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:23962000-23968800	Weak transcription	NHEK	skin
22	chr3:23962000-23969000	Weak transcription	Fetal Brain Male	brain
23	chr3:23962000-23969000	Weak transcription	Fetal Kidney	kidney
24	chr3:23962000-23969400	Weak transcription	Pancreas	Pancrea
25	chr3:23962000-23969600	Weak transcription	Gastric	stomach
26	chr3:23962000-23970000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:23962000-23972800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:23962000-23974800	Weak transcription	Brain Substantia Nigra	brain
29	chr3:23962000-23977800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:23962000-23985600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:23962200-23965400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:23962200-23965400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:23962200-23965800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:23962200-23967800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:23962200-23968800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:23962200-23969000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:23962200-23970000	Weak transcription	Hela-S3	cervix
38	chr3:23962400-23965200	Weak transcription	Osteobl	bone
39	chr3:23962400-23965600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:23962400-23968800	Weak transcription	HepG2	liver
41	chr3:23962400-23968800	Weak transcription	NHDF-Ad	bronchial
42	chr3:23962600-23965200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:23962600-23966000	Weak transcription	Fetal Intestine Large	intestine
44	chr3:23962600-23967200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:23962600-23970000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:23962800-23965200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:23962800-23965400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:23962800-23968800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:23963000-23965000	Strong transcription	Fetal Intestine Small	intestine
50	chr3:23963000-23965400	Weak transcription	HUVEC	blood vessel

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