Variant report

Variant	rs4713996
Chromosome Location	chr6:36629714-36629715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36561045..36564139-chr6:36628780..36632621,3	K562	blood:
2	chr6:36628763..36632041-chr6:36634655..36636899,4	MCF-7	breast:
3	chr6:36609790..36612308-chr6:36629245..36631254,2	MCF-7	breast:
4	chr6:36586935..36591070-chr6:36628683..36631077,3	K562	blood:
5	chr6:36628825..36632720-chr6:36633397..36637228,8	MCF-7	breast:
6	chr6:36627657..36630518-chr6:36646219..36647988,2	K562	blood:
7	chr6:36602002..36604022-chr6:36629125..36630980,2	MCF-7	breast:
8	chr6:36623725..36625807-chr6:36629087..36632013,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000263894	Chromatin interaction
ENSG00000124762	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10807170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176320	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs3176323	0.80[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3176334	0.85[JPT][hapmap]
rs4711456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711457	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713999	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];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6930083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs733590	0.93[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9394368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4713996	CDKN1A	cis	multi-tissue	Pritchard
rs4713996		cis	Lymphoblastoid	GTEx
rs4713996	CDKN1A	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36627400-36629800	Bivalent Enhancer	Fetal Thymus	thymus
2	chr6:36627800-36634000	Weak transcription	HMEC	breast
3	chr6:36627800-36634000	Weak transcription	HSMM	muscle
4	chr6:36628000-36631200	Enhancers	Primary B cells from cord blood	blood
5	chr6:36628200-36636600	Enhancers	Primary B cells from peripheral blood	blood
6	chr6:36628600-36631200	Enhancers	Gastric	stomach
7	chr6:36628800-36629800	Bivalent Enhancer	Primary T cells from cord blood	blood
8	chr6:36628800-36630200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:36628800-36631200	Enhancers	Thymus	Thymus
10	chr6:36629000-36630000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:36629000-36630000	Weak transcription	Colonic Mucosa	Colon
12	chr6:36629000-36630400	Enhancers	Duodenum Mucosa	Duodenum
13	chr6:36629000-36630800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:36629000-36631200	Enhancers	Esophagus	oesophagus
15	chr6:36629000-36631400	Enhancers	Fetal Intestine Large	intestine
16	chr6:36629000-36633600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:36629000-36633800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr6:36629200-36629800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
19	chr6:36629200-36629800	Enhancers	Fetal Heart	heart
20	chr6:36629200-36630200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:36629200-36630200	Weak transcription	Placenta	Placenta
22	chr6:36629200-36630200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:36629200-36630200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr6:36629200-36630400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
25	chr6:36629200-36630400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:36629200-36630600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:36629200-36630600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:36629200-36630800	Weak transcription	Brain Anterior Caudate	brain
29	chr6:36629200-36631000	Enhancers	Stomach Mucosa	stomach
30	chr6:36629200-36631200	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr6:36629200-36633400	Weak transcription	Ovary	ovary
32	chr6:36629200-36634200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:36629200-36634200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:36629200-36634600	Weak transcription	Liver	Liver
35	chr6:36629200-36634800	Weak transcription	Right Atrium	heart
36	chr6:36629200-36635000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr6:36629200-36635000	Weak transcription	Right Ventricle	heart
38	chr6:36629400-36629800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:36629400-36629800	Weak transcription	Fetal Intestine Small	intestine
40	chr6:36629400-36629800	Weak transcription	Pancreas	Pancrea
41	chr6:36629400-36630600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:36629400-36631200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr6:36629400-36634600	Weak transcription	Adipose Nuclei	Adipose
44	chr6:36629600-36629800	Bivalent Enhancer	Fetal Muscle Leg	muscle
45	chr6:36629600-36629800	Flanking Active TSS	GM12878-XiMat	blood
46	chr6:36629600-36630200	Enhancers	Hela-S3	cervix
47	chr6:36629600-36630200	Bivalent Enhancer	HepG2	liver
48	chr6:36629600-36630600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr6:36629600-36631200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr6:36629600-36631600	Weak transcription	K562	blood

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