Variant report

Variant	rs2836436
Chromosome Location	chr21:39861730-39861731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:39861096..39863150-chr21:39872187..39874379,2	K562	blood:
2	chr21:39860012..39862527-chr21:39874873..39876788,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231480	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1041795	0.82[MEX][hapmap]
rs2070351	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2898353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs960819	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9981032	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]

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	nsv1059340	chr21:39817504-39881353	Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1064436	chr21:39846571-39875576	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2836436	PCP4	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:39855000-39861800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr21:39856400-39862200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr21:39857600-39861800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr21:39858000-39862400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr21:39858000-39864000	Enhancers	Fetal Heart	heart
6	chr21:39858400-39862000	Enhancers	Stomach Mucosa	stomach
7	chr21:39858800-39862800	Enhancers	Adipose Nuclei	Adipose
8	chr21:39859000-39862400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr21:39859400-39862800	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr21:39859400-39863800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr21:39859600-39861800	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr21:39859600-39862000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr21:39859600-39862000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr21:39859600-39865600	Weak transcription	Fetal Muscle Leg	muscle
15	chr21:39859800-39862000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr21:39859800-39862200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr21:39859800-39862400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr21:39859800-39863000	Enhancers	Fetal Thymus	thymus
19	chr21:39859800-39864000	Weak transcription	Fetal Lung	lung
20	chr21:39859800-39864200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr21:39860000-39861800	Enhancers	Fetal Intestine Large	intestine
22	chr21:39860000-39862200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr21:39860200-39862400	Weak transcription	Lung	lung
24	chr21:39860200-39862400	Weak transcription	Right Ventricle	heart
25	chr21:39860200-39865400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr21:39860200-39865600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr21:39860200-39865600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr21:39860400-39861800	Weak transcription	Spleen	Spleen
29	chr21:39860400-39879000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr21:39860600-39861800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr21:39860600-39861800	Enhancers	Fetal Intestine Small	intestine
32	chr21:39860600-39862000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr21:39860800-39861800	Enhancers	Duodenum Mucosa	Duodenum
34	chr21:39860800-39862000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr21:39861000-39862000	Enhancers	Colonic Mucosa	Colon
36	chr21:39861000-39862400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr21:39861000-39862600	Genic enhancers	Primary hematopoietic stem cells	blood
38	chr21:39861000-39863600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr21:39861000-39863800	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr21:39861000-39865800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr21:39861000-39867600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr21:39861200-39861800	Enhancers	Right Atrium	heart
43	chr21:39861200-39861800	Enhancers	Small Intestine	intestine
44	chr21:39861200-39861800	Enhancers	NHEK	skin
45	chr21:39861200-39862600	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr21:39861200-39863200	Enhancers	H1 Cell Line	embryonic stem cell
47	chr21:39861200-39866200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr21:39861400-39861800	Weak transcription	Gastric	stomach
49	chr21:39861400-39862000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr21:39861400-39862000	Enhancers	HMEC	breast

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