Variant report

Variant	rs4713999
Chromosome Location	chr6:36633069-36633070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36631478..36636279-chr6:36645838..36648638,4	K562	blood:
2	chr6:36630192..36637203-chr6:36642841..36649451,13	K562	blood:
3	chr6:36609889..36612483-chr6:36632704..36634800,2	MCF-7	breast:
4	chr6:36631889..36633994-chr6:36649894..36652299,3	K562	blood:

Variant related genes	Relation type
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10807170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2395655	0.81[MEX][hapmap]
rs3176320	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs3176323	0.81[CEU][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs3176334	0.87[TSI][hapmap]
rs4711456	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4711457	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4713996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4714001	0.92[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6930083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs733590	0.93[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap]
rs9394368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9462210	0.83[YRI][hapmap]

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	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4713999	CDKN1A	cis	Lymphoblastoid	GTEx
rs4713999	PI16	cis	parietal	SCAN
rs4713999	LHFPL5	cis	cerebellum	SCAN
rs4713999		cis	Lymphoblastoid	GTEx
rs4713999	CDKN1A	cis	multi-tissue	Pritchard
rs4713999	CDKN1A	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36627800-36634000	Weak transcription	HMEC	breast
2	chr6:36627800-36634000	Weak transcription	HSMM	muscle
3	chr6:36628200-36636600	Enhancers	Primary B cells from peripheral blood	blood
4	chr6:36629000-36633600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:36629000-36633800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:36629200-36633400	Weak transcription	Ovary	ovary
7	chr6:36629200-36634200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:36629200-36634200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:36629200-36634600	Weak transcription	Liver	Liver
10	chr6:36629200-36634800	Weak transcription	Right Atrium	heart
11	chr6:36629200-36635000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr6:36629200-36635000	Weak transcription	Right Ventricle	heart
13	chr6:36629400-36634600	Weak transcription	Adipose Nuclei	Adipose
14	chr6:36630800-36634200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:36630800-36634200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:36630800-36635000	Weak transcription	Fetal Heart	heart
17	chr6:36631000-36634000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:36631000-36634200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:36631000-36634200	Weak transcription	Colonic Mucosa	Colon
20	chr6:36631000-36644000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:36631200-36633600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:36631200-36634000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:36631200-36634000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:36631200-36634000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:36631200-36634000	Weak transcription	Pancreas	Pancrea
26	chr6:36631200-36634000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr6:36631200-36634200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:36631200-36634200	Weak transcription	Esophagus	oesophagus
29	chr6:36631400-36633800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:36631400-36633800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:36631400-36633800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:36631400-36634000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:36631400-36634000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:36631400-36634000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:36631400-36634000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:36631400-36634000	Weak transcription	Fetal Intestine Large	intestine
37	chr6:36631400-36634000	Weak transcription	NHEK	skin
38	chr6:36631400-36634200	Weak transcription	Brain Anterior Caudate	brain
39	chr6:36631400-36634200	Weak transcription	Fetal Intestine Small	intestine
40	chr6:36631400-36634200	Weak transcription	Placenta	Placenta
41	chr6:36631400-36634200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr6:36631600-36633200	Flanking Active TSS	GM12878-XiMat	blood
43	chr6:36631600-36634000	Weak transcription	Hela-S3	cervix
44	chr6:36631800-36633600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:36631800-36634200	Weak transcription	K562	blood
46	chr6:36631800-36634200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr6:36631800-36634400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr6:36631800-36635600	Weak transcription	Fetal Thymus	thymus
49	chr6:36632000-36638800	Weak transcription	Duodenum Mucosa	Duodenum
50	chr6:36632200-36633200	Weak transcription	HepG2	liver

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