Variant report

Variant	rs2920672
Chromosome Location	chr8:6305462-6305463
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1129703	0.82[EUR][1000 genomes]
rs1129704	0.82[EUR][1000 genomes]
rs1129706	0.82[EUR][1000 genomes]
rs12546890	0.83[EUR][1000 genomes]
rs1373306	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1373307	0.82[EUR][1000 genomes]
rs17076812	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17536777	0.81[ASN][1000 genomes]
rs17609194	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1867386	0.82[EUR][1000 genomes]
rs1868551	0.84[EUR][1000 genomes]
rs2034143	0.84[EUR][1000 genomes]
rs2083914	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2166006	0.82[EUR][1000 genomes]
rs2440408	0.83[EUR][1000 genomes]
rs2440411	0.82[EUR][1000 genomes]
rs2440412	0.82[EUR][1000 genomes]
rs2440414	0.84[EUR][1000 genomes]
rs2440416	0.80[EUR][1000 genomes]
rs2442502	0.82[EUR][1000 genomes]
rs2442503	0.83[EUR][1000 genomes]
rs2442505	0.82[EUR][1000 genomes]
rs2442506	0.82[EUR][1000 genomes]
rs2442507	0.82[EUR][1000 genomes]
rs2442510	0.80[EUR][1000 genomes]
rs2442511	0.80[EUR][1000 genomes]
rs2515572	0.82[EUR][1000 genomes]
rs2515576	0.80[EUR][1000 genomes]
rs2916749	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920668	0.81[EUR][1000 genomes]
rs2920669	0.84[EUR][1000 genomes]
rs2920671	0.82[EUR][1000 genomes]
rs2922821	0.80[EUR][1000 genomes]
rs2922822	0.82[EUR][1000 genomes]
rs2922823	0.83[EUR][1000 genomes]
rs2922824	0.83[EUR][1000 genomes]
rs2979648	0.81[EUR][1000 genomes]
rs2979650	0.81[EUR][1000 genomes]
rs3020270	0.91[EUR][1000 genomes]
rs3020278	0.81[EUR][1000 genomes]
rs6993448	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7018378	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890034	chr8:5926632-6427868	Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv1026004	chr8:6144798-6307692	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv539431	chr8:6144798-6307692	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv933107	chr8:6173244-6312807	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv482828	chr8:6182711-6355710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv890055	chr8:6237397-6351252	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv531468	chr8:6248682-6309194	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2920672	MCPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6265000-6339200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr8:6282800-6313400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr8:6287200-6309200	Weak transcription	Fetal Brain Male	brain
4	chr8:6287600-6306600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr8:6287600-6307600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:6287600-6344400	Weak transcription	Small Intestine	intestine
7	chr8:6289000-6308000	Strong transcription	Dnd41	blood
8	chr8:6289200-6306200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr8:6289200-6306400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr8:6289400-6306600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr8:6291800-6305800	Weak transcription	Stomach Mucosa	stomach
12	chr8:6297800-6306000	Strong transcription	Adipose Nuclei	Adipose
13	chr8:6297800-6306000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr8:6297800-6307600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr8:6298000-6307600	Strong transcription	GM12878-XiMat	blood
16	chr8:6299200-6308000	Strong transcription	Fetal Thymus	thymus
17	chr8:6300000-6306200	Strong transcription	Primary T cells from cord blood	blood
18	chr8:6300000-6306200	Strong transcription	Fetal Lung	lung
19	chr8:6300800-6305800	Strong transcription	Brain Hippocampus Middle	brain
20	chr8:6301000-6309600	Weak transcription	Fetal Heart	heart
21	chr8:6301000-6338400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr8:6301400-6308800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr8:6301600-6306200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr8:6302400-6305800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr8:6302600-6307200	Weak transcription	HMEC	breast
26	chr8:6302800-6313800	Weak transcription	Brain Angular Gyrus	brain
27	chr8:6302800-6339800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr8:6303000-6307200	Weak transcription	Thymus	Thymus
29	chr8:6303000-6307200	Weak transcription	HSMM	muscle
30	chr8:6303000-6307800	Weak transcription	Aorta	Aorta
31	chr8:6303000-6309000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr8:6303000-6310200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr8:6303000-6311800	Weak transcription	NHDF-Ad	bronchial
34	chr8:6303000-6312000	Weak transcription	HSMMtube	muscle
35	chr8:6303000-6312400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr8:6303000-6313400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr8:6303000-6313800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr8:6303000-6317200	Weak transcription	Brain Substantia Nigra	brain
39	chr8:6303000-6317800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr8:6303000-6319400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr8:6303000-6321000	Weak transcription	Psoas Muscle	Psoas
42	chr8:6303000-6321000	Weak transcription	Hela-S3	cervix
43	chr8:6303000-6322800	Weak transcription	Ovary	ovary
44	chr8:6303000-6322800	Weak transcription	Spleen	Spleen
45	chr8:6303000-6325000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr8:6303000-6325200	Weak transcription	Pancreas	Pancrea
47	chr8:6303000-6338200	Weak transcription	Gastric	stomach
48	chr8:6303000-6338200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr8:6303000-6338400	Weak transcription	Colonic Mucosa	Colon
50	chr8:6303000-6338400	Weak transcription	Right Ventricle	heart

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