Variant report

Variant	rs12680048
Chromosome Location	chr8:6340660-6340661
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	chr8:6339705..6342364-chr8:6348069..6350911,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11137033	0.96[ASN][1000 genomes]
rs12674488	0.92[AFR][1000 genomes]
rs12677501	1.00[ASN][1000 genomes]
rs12679619	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13248420	0.81[ASN][1000 genomes]
rs13267816	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13281793	0.81[ASN][1000 genomes]
rs13282116	0.81[ASN][1000 genomes]
rs17077094	0.81[ASN][1000 genomes]
rs17077109	1.00[ASN][1000 genomes]
rs17613024	0.83[ASN][1000 genomes]
rs1868555	0.92[ASN][1000 genomes]
rs2440392	0.87[ASN][1000 genomes]
rs2440396	0.89[ASN][1000 genomes]
rs2440397	0.88[ASN][1000 genomes]
rs2440428	0.93[ASN][1000 genomes]
rs2442483	0.91[ASN][1000 genomes]
rs2442491	0.87[ASN][1000 genomes]
rs2442493	0.89[ASN][1000 genomes]
rs2515585	0.87[ASN][1000 genomes]
rs2920674	0.98[ASN][1000 genomes]
rs2920677	0.93[ASN][1000 genomes]
rs2920678	0.93[ASN][1000 genomes]
rs2920689	0.93[ASN][1000 genomes]
rs2922811	0.93[ASN][1000 genomes]
rs2922813	0.94[ASN][1000 genomes]
rs2922814	0.94[ASN][1000 genomes]
rs2922815	0.94[ASN][1000 genomes]
rs2979664	0.93[ASN][1000 genomes]
rs3020289	0.87[ASN][1000 genomes]
rs34009442	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34635086	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34748476	0.82[ASN][1000 genomes]
rs35150903	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35248379	0.87[ASN][1000 genomes]
rs57804372	0.89[ASN][1000 genomes]
rs58679306	0.94[ASN][1000 genomes]
rs6989935	0.88[ASN][1000 genomes]
rs73520657	0.96[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	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
7	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
8	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
9	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
10	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
11	nsv890056	chr8:6314486-6343727	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv890057	chr8:6317165-6427868	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1025860	chr8:6328628-6360743	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv890058	chr8:6329510-6367302	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12680048	MCPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6287600-6344400	Weak transcription	Small Intestine	intestine
2	chr8:6304400-6360200	Weak transcription	Esophagus	oesophagus
3	chr8:6308000-6372600	Weak transcription	HMEC	breast
4	chr8:6316400-6345600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr8:6317800-6380200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr8:6321800-6342000	Weak transcription	Aorta	Aorta
7	chr8:6321800-6343800	Weak transcription	Hela-S3	cervix
8	chr8:6322000-6346800	Weak transcription	Colon Smooth Muscle	Colon
9	chr8:6323400-6342000	Weak transcription	NHEK	skin
10	chr8:6325800-6374400	Weak transcription	K562	blood
11	chr8:6331400-6345600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr8:6333000-6342000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr8:6335000-6344200	Weak transcription	NHLF	lung
14	chr8:6335000-6345200	Weak transcription	Ovary	ovary
15	chr8:6335400-6341200	Weak transcription	Fetal Lung	lung
16	chr8:6335600-6344400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr8:6336800-6377600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr8:6337000-6342200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr8:6337000-6342400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr8:6337800-6342200	Strong transcription	Lung	lung
21	chr8:6337800-6342400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr8:6337800-6347600	Strong transcription	Primary T cells from cord blood	blood
23	chr8:6338000-6340800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr8:6338000-6342400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr8:6338000-6342400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr8:6338000-6342600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr8:6338000-6343600	Strong transcription	GM12878-XiMat	blood
28	chr8:6338200-6340800	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr8:6338200-6341000	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr8:6338200-6341000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr8:6338200-6341000	Strong transcription	Brain Hippocampus Middle	brain
32	chr8:6338200-6341000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr8:6338200-6341000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr8:6338200-6341200	Strong transcription	Primary B cells from cord blood	blood
35	chr8:6338200-6341800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr8:6338200-6342000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr8:6338200-6342400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr8:6338200-6342400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr8:6338200-6342400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr8:6338200-6342400	Strong transcription	Adipose Nuclei	Adipose
41	chr8:6338200-6342400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr8:6338200-6342400	Strong transcription	Rectal Smooth Muscle	rectum
43	chr8:6338200-6342400	Strong transcription	HSMM	muscle
44	chr8:6338200-6343400	Strong transcription	Fetal Intestine Large	intestine
45	chr8:6338200-6343400	Strong transcription	Thymus	Thymus
46	chr8:6338400-6340800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr8:6338400-6341200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr8:6338400-6341200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr8:6338400-6341200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr8:6338400-6341400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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