Variant report

Variant	rs2959777
Chromosome Location	chr8:6433935-6433936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:6262835..6265466-chr8:6433690..6436304,2	K562	blood:
2	chr8:6433156..6436066-chr8:6444160..6446250,2	K562	blood:

Variant related genes	Relation type
ENSG00000147316	Chromatin interaction
ENSG00000246089	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12546205	1.00[JPT][hapmap]
rs17063453	0.84[ASN][1000 genomes]
rs17077573	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17554274	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17624865	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2442551	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2515514	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2922840	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2922841	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2922842	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2922843	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2922845	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2959776	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7820827	1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv3506199	chr8:6116693-6536592	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
4	esv3506200	chr8:6116693-6536592	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv933282	chr8:6261036-6440592	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1015981	chr8:6286575-6578450	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1021684	chr8:6350091-6809455	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	esv2422383	chr8:6362389-6781593	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv610004	chr8:6402366-6772913	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
11	nsv1029241	chr8:6411300-6761720	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2959777	MCPH1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6364200-6478200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr8:6416800-6442400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr8:6417600-6442800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:6419000-6462400	Weak transcription	GM12878-XiMat	blood
5	chr8:6421000-6435400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr8:6421200-6436200	Weak transcription	Right Atrium	heart
7	chr8:6421600-6462800	Weak transcription	Primary B cells from cord blood	blood
8	chr8:6424200-6442600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr8:6424400-6434400	Weak transcription	Lung	lung
10	chr8:6424400-6442800	Weak transcription	NHEK	skin
11	chr8:6424800-6436600	Weak transcription	Esophagus	oesophagus
12	chr8:6424800-6440600	Weak transcription	Primary T cells from cord blood	blood
13	chr8:6424800-6442200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr8:6424800-6442600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr8:6424800-6451600	Weak transcription	Spleen	Spleen
16	chr8:6426400-6442800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr8:6426600-6442800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr8:6427600-6435600	Weak transcription	Ovary	ovary
19	chr8:6427800-6451200	Weak transcription	Adipose Nuclei	Adipose
20	chr8:6428200-6435400	Weak transcription	Aorta	Aorta
21	chr8:6428200-6435600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr8:6428200-6440800	Weak transcription	Thymus	Thymus
23	chr8:6428200-6441000	Weak transcription	Fetal Kidney	kidney
24	chr8:6428200-6442200	Weak transcription	HSMM	muscle
25	chr8:6428200-6450800	Weak transcription	Left Ventricle	heart
26	chr8:6428400-6439400	Weak transcription	Fetal Stomach	stomach
27	chr8:6429000-6437800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr8:6429400-6435400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr8:6430200-6435000	Weak transcription	Brain Hippocampus Middle	brain
30	chr8:6430400-6451000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr8:6430800-6434000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr8:6431000-6451000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr8:6431800-6434000	Enhancers	K562	blood
34	chr8:6431800-6441200	Weak transcription	Hela-S3	cervix
35	chr8:6432200-6453800	Weak transcription	Fetal Intestine Small	intestine
36	chr8:6432400-6434600	Weak transcription	Dnd41	blood
37	chr8:6432400-6436600	Enhancers	Placenta	Placenta
38	chr8:6432400-6440200	Weak transcription	Fetal Thymus	thymus
39	chr8:6432400-6457600	Weak transcription	Gastric	stomach
40	chr8:6432600-6434400	Weak transcription	Fetal Muscle Leg	muscle
41	chr8:6432800-6434600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr8:6433200-6434000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr8:6433200-6434600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr8:6433200-6435000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr8:6433200-6435200	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr8:6433200-6436600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr8:6433400-6434400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr8:6433400-6434600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr8:6433400-6435600	Weak transcription	Pancreas	Pancrea
50	chr8:6433600-6434800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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