Variant report

Variant	rs4714001
Chromosome Location	chr6:36638175-36638176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36633841..36635669-chr6:36637312..36639563,2	K562	blood:
2	chr6:36600535..36602963-chr6:36638081..36640016,2	MCF-7	breast:
3	chr6:36637280..36638995-chr6:36645495..36647593,2	K562	blood:

Variant related genes	Relation type
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10807170	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2395655	0.82[AMR][1000 genomes]
rs3176320	0.85[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3176323	0.85[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3176334	0.85[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4135240	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4711456	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711457	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713996	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]
rs4713999	0.92[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6930083	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs733590	0.87[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9394368	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	nsv602946	chr6:36633160-36641478	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
4	nsv602947	chr6:36637597-36641157	Enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4714001	CDKN1A	cis	Lymphoblastoid	GTEx
rs4714001	CDKN1A	cis	multi-tissue	Pritchard
rs4714001		cis	Lymphoblastoid	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36631000-36644000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:36632000-36638800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:36633200-36640200	Enhancers	HepG2	liver
4	chr6:36634800-36638200	Enhancers	Fetal Muscle Trunk	muscle
5	chr6:36635200-36643800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:36635400-36639600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:36635400-36644000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:36635400-36645600	Weak transcription	Small Intestine	intestine
9	chr6:36635600-36644000	Weak transcription	Hela-S3	cervix
10	chr6:36635800-36639800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:36636000-36640800	Enhancers	Fetal Intestine Small	intestine
12	chr6:36636400-36643800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:36636400-36643800	Weak transcription	NH-A	brain
14	chr6:36636800-36641000	Enhancers	Fetal Intestine Large	intestine
15	chr6:36637000-36638600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr6:36637000-36643800	Weak transcription	Osteobl	bone
17	chr6:36637200-36638200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:36637200-36638400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:36637200-36641600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:36637200-36641600	Weak transcription	GM12878-XiMat	blood
21	chr6:36637200-36643600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:36637200-36643800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:36637200-36643800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr6:36637200-36643800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:36637200-36643800	Weak transcription	HSMM	muscle
26	chr6:36637400-36639800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:36637400-36642600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:36637800-36639200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:36637800-36642600	Weak transcription	HSMMtube	muscle
30	chr6:36637800-36643400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:36637800-36643400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:36637800-36643800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:36637800-36643800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:36638000-36638800	Enhancers	Ovary	ovary

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