Variant report

Variant	rs4619736
Chromosome Location	chr3:23992383-23992384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
2	chr3:23992186..23994310-chr3:24012801..24015062,2	MCF-7	breast:
3	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
4	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197885	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000174748	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1135452	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11922609	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2001209	0.91[ASN][1000 genomes]
rs5001573	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6773828	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6778970	0.84[ASN][1000 genomes]
rs6800407	0.84[ASN][1000 genomes]
rs72627066	0.84[ASN][1000 genomes]
rs7633520	0.91[ASN][1000 genomes]
rs9755750	0.91[ASN][1000 genomes]
rs9862416	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4619736	NR1D2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23988000-23995000	Weak transcription	Spleen	Spleen
2	chr3:23988200-23993800	Enhancers	Brain Substantia Nigra	brain
3	chr3:23988200-24000600	Weak transcription	Fetal Brain Male	brain
4	chr3:23988200-24003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:23988400-23992400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr3:23988400-23993600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr3:23988400-23995200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:23988400-23996000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:23988400-23996400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr3:23988400-24003000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:23988400-24003400	Weak transcription	Fetal Kidney	kidney
12	chr3:23988600-23994000	Enhancers	Psoas Muscle	Psoas
13	chr3:23988600-23996000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:23989000-23993800	Enhancers	Liver	Liver
15	chr3:23989000-23996400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:23989000-23997800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:23989000-23998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:23989200-23992800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:23989200-23995000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:23989200-23996000	Enhancers	Adipose Nuclei	Adipose
21	chr3:23989200-23996200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:23989200-23996200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:23989200-24000600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:23989200-24003000	Weak transcription	Fetal Thymus	thymus
25	chr3:23989200-24007400	Weak transcription	Fetal Brain Female	brain
26	chr3:23989200-24018000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:23989200-24020600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:23989400-23992800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:23989400-23993800	Enhancers	Brain Anterior Caudate	brain
31	chr3:23989400-23994400	Enhancers	Brain Angular Gyrus	brain
32	chr3:23989400-23996000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:23989400-23996200	Enhancers	Brain Hippocampus Middle	brain
34	chr3:23989600-24003400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:23989600-24003400	Weak transcription	Esophagus	oesophagus
36	chr3:23989600-24003600	Weak transcription	Colonic Mucosa	Colon
37	chr3:23989800-23993200	Weak transcription	Brain Germinal Matrix	brain
38	chr3:23989800-23993400	Weak transcription	Gastric	stomach
39	chr3:23989800-23994600	Weak transcription	Lung	lung
40	chr3:23989800-23995600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:23989800-23996000	Weak transcription	Osteobl	bone
42	chr3:23989800-24017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:23990000-24000200	Weak transcription	HUVEC	blood vessel
44	chr3:23990000-24001000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr3:23990400-23995400	Weak transcription	Aorta	Aorta
46	chr3:23990400-23996200	Weak transcription	Placenta	Placenta
47	chr3:23990400-23997600	Weak transcription	NH-A	brain
48	chr3:23990600-23992800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:23990600-23995600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr3:23990600-23999800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links