Variant report

Variant	rs6800407
Chromosome Location	chr3:23957000-23957001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr3:23956868-23957399	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:23956995-23957349	HCT-116	colon:	n/a	n/a
3	HEY1	chr3:23956996-23957428	HepG2	liver:	n/a	n/a
4	MAFK	chr3:23956888-23957491	K562	blood:	n/a	n/a
5	MAZ	chr3:23956817-23957514	K562	blood:	n/a	n/a
6	RCOR1	chr3:23956779-23959303	K562	blood:	n/a	n/a
7	JUND	chr3:23956927-23959302	K562	blood:	n/a	chr3:23957807-23957821 chr3:23957714-23957723
8	MXI1	chr3:23956869-23957393	K562	blood:	n/a	n/a
9	POLR2A	chr3:23956956-23957408	SK-N-SH	brain:	n/a	n/a
10	CREB1	chr3:23956849-23957394	HepG2	liver:	n/a	n/a
11	REST	chr3:23956836-23959890	H1-neurons	neurons:	n/a	chr3:23958595-23958608 chr3:23958203-23958212
12	TEAD4	chr3:23956932-23959905	K562	blood:	n/a	n/a
13	STAT3	chr3:23956974-23957303	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:23956587..23958412-chr3:24004653..24006341,2	K562	blood:
2	chr3:23956507..23958836-chr3:25705831..25708315,2	K562	blood:
3	chr3:23846380..23850116-chr3:23956700..23960461,6	MCF-7	breast:
4	chr3:23956080..23959048-chr3:23995915..23997492,2	MCF-7	breast:
5	chr3:23852479..23855481-chr3:23956917..23960502,4	MCF-7	breast:
6	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
7	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:

Variant related genes	Relation type
RPL15	TF binding region
ENSG00000197885	Chromatin interaction
ENSG00000077097	Chromatin interaction
ENSG00000223791	Chromatin interaction
ENSG00000264219	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000170142	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1133926	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1135452	0.88[ASN][1000 genomes]
rs1136155	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11710647	0.82[EUR][1000 genomes]
rs11710679	1.00[CEU][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11711380	0.87[EUR][1000 genomes]
rs11713246	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs11718625	0.82[JPT][hapmap]
rs12497944	0.82[JPT][hapmap]
rs13314607	0.87[EUR][1000 genomes]
rs13318927	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13325754	0.92[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs17787211	0.93[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2001209	0.81[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs28623591	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34476593	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35711415	0.83[EUR][1000 genomes]
rs4131864	0.82[JPT][hapmap]
rs4619736	0.84[ASN][1000 genomes]
rs5001573	0.88[ASN][1000 genomes]
rs61645368	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62253361	0.83[EUR][1000 genomes]
rs62253380	0.82[EUR][1000 genomes]
rs62253387	0.82[EUR][1000 genomes]
rs6550809	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6773828	0.88[ASN][1000 genomes]
rs6778970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787216	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6789983	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72627066	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73825116	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73825124	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73825170	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73825178	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73825181	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7629325	0.92[EUR][1000 genomes]
rs7633520	0.93[ASN][1000 genomes]
rs7637968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8933	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9755750	0.93[ASN][1000 genomes]
rs9815334	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9834166	0.92[EUR][1000 genomes]
rs9836860	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9836970	1.00[CEU][hapmap];0.85[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9838694	0.82[EUR][1000 genomes]
rs9850255	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9856727	0.87[EUR][1000 genomes]
rs9857442	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9862416	0.88[ASN][1000 genomes]
rs9863674	0.85[EUR][1000 genomes]
rs9875213	0.85[EUR][1000 genomes]
rs9876561	1.00[CEU][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6800407	NR1D2	Cis_1M	lymphoblastoid	RTeQTL
rs6800407	NR1D2	cis	Frontal Cortex	GTEx
rs6800407	NKIRAS1	Cis_1M	lymphoblastoid	RTeQTL
rs6800407	NR1D2	cis	Temporal Cortex	GTEx
rs6800407	NR1D2	cis	Brain Pons	GTEx

Chromatin state (count:164 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23923400-23957000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:23924200-23957800	Weak transcription	Esophagus	oesophagus
3	chr3:23924200-23957800	Weak transcription	Lung	lung
4	chr3:23928000-23957200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:23928800-23957400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:23935000-23957400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:23936800-23957200	Weak transcription	Brain Substantia Nigra	brain
8	chr3:23940800-23957000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:23940800-23957200	Weak transcription	Right Ventricle	heart
10	chr3:23942600-23957000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:23942800-23957000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:23943000-23957200	Weak transcription	Primary T cells from cord blood	blood
13	chr3:23944600-23957200	Weak transcription	HSMMtube	muscle
14	chr3:23944800-23957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:23946000-23957000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:23946000-23957800	Weak transcription	Gastric	stomach
17	chr3:23952000-23957200	Weak transcription	Spleen	Spleen
18	chr3:23952000-23957800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:23952400-23957200	Weak transcription	HSMM	muscle
20	chr3:23952400-23957600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:23952600-23957000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:23952600-23957400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:23952800-23957000	Weak transcription	Fetal Brain Female	brain
24	chr3:23952800-23957200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:23952800-23957200	Weak transcription	Placenta	Placenta
26	chr3:23953000-23957000	Weak transcription	Fetal Stomach	stomach
27	chr3:23955200-23957200	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr3:23955200-23957200	Weak transcription	HUVEC	blood vessel
29	chr3:23955400-23957000	Enhancers	A549	lung
30	chr3:23955400-23957200	Enhancers	NHEK	skin
31	chr3:23955800-23957000	Enhancers	Brain Cingulate Gyrus	brain
32	chr3:23956000-23957000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:23956000-23957000	Enhancers	Fetal Lung	lung
34	chr3:23956000-23957000	Enhancers	Hela-S3	cervix
35	chr3:23956000-23957000	Enhancers	HMEC	breast
36	chr3:23956000-23957000	Enhancers	Osteobl	bone
37	chr3:23956000-23957200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:23956000-23957400	Enhancers	Fetal Heart	heart
39	chr3:23956000-23957400	Flanking Active TSS	GM12878-XiMat	blood
40	chr3:23956000-23957800	Enhancers	Small Intestine	intestine
41	chr3:23956200-23957200	Enhancers	Primary hematopoietic stem cells	blood
42	chr3:23956200-23957200	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr3:23956200-23957200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:23956200-23957800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:23956400-23957000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:23956400-23957000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:23956400-23957000	Enhancers	Colon Smooth Muscle	Colon
48	chr3:23956400-23957000	Enhancers	Fetal Kidney	kidney
49	chr3:23956400-23957000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:23956400-23957000	Enhancers	Skeletal Muscle Female	skeletal muscle

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