Variant report

Variant	rs2440402
Chromosome Location	chr8:6321054-6321055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1867385	0.84[AFR][1000 genomes]
rs2440392	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2440399	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2440400	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2440401	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2440403	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2440408	0.84[AFR][1000 genomes]
rs2442483	0.90[AFR][1000 genomes]
rs2442489	0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2442490	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2442492	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2442496	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2442499	0.86[EUR][1000 genomes]
rs2442500	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2442502	0.84[AFR][1000 genomes]
rs2442503	0.84[AFR][1000 genomes]
rs2515576	0.86[AFR][1000 genomes]
rs2515581	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2515582	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2515583	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2515587	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2916733	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916734	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2916737	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2916738	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916739	0.85[EUR][1000 genomes]
rs2916740	0.85[EUR][1000 genomes]
rs2916741	0.85[EUR][1000 genomes]
rs2916742	0.85[EUR][1000 genomes]
rs2916743	0.85[EUR][1000 genomes]
rs2916745	0.85[EUR][1000 genomes]
rs2916746	0.89[EUR][1000 genomes]
rs2920656	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2920658	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2920659	0.85[EUR][1000 genomes]
rs2920660	0.86[EUR][1000 genomes]
rs2920661	0.85[EUR][1000 genomes]
rs2920662	0.85[EUR][1000 genomes]
rs2920677	0.89[AFR][1000 genomes]
rs2920689	0.90[AFR][1000 genomes]
rs2922813	0.90[AFR][1000 genomes]
rs2922814	0.86[AFR][1000 genomes]
rs2922815	0.90[AFR][1000 genomes]
rs2922818	0.85[EUR][1000 genomes]
rs2922819	0.85[EUR][1000 genomes]
rs2922820	0.84[EUR][1000 genomes]
rs2979651	0.83[EUR][1000 genomes]
rs2979652	0.85[EUR][1000 genomes]
rs2979653	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2979655	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2979656	0.92[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2979664	0.91[AFR][1000 genomes]
rs3020281	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3020289	0.83[AFR][1000 genomes]
rs7001036	0.84[EUR][1000 genomes]
rs7001056	0.85[EUR][1000 genomes]
rs7824209	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1023443	chr8:6319260-6332157	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active 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
rs2440402	MCPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 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	chr8:6287600-6344400	Weak transcription	Small Intestine	intestine
3	chr8:6301000-6338400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr8:6302800-6339800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr8:6303000-6322800	Weak transcription	Ovary	ovary
6	chr8:6303000-6322800	Weak transcription	Spleen	Spleen
7	chr8:6303000-6325000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr8:6303000-6325200	Weak transcription	Pancreas	Pancrea
9	chr8:6303000-6338200	Weak transcription	Gastric	stomach
10	chr8:6303000-6338200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr8:6303000-6338400	Weak transcription	Colonic Mucosa	Colon
12	chr8:6303000-6338400	Weak transcription	Right Ventricle	heart
13	chr8:6303000-6339400	Weak transcription	Placenta	Placenta
14	chr8:6303200-6322600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr8:6303200-6322800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr8:6303200-6339400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr8:6303200-6339400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr8:6303200-6340000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr8:6303400-6321200	Weak transcription	HUVEC	blood vessel
20	chr8:6303600-6321600	Weak transcription	Brain Germinal Matrix	brain
21	chr8:6303800-6338400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr8:6304000-6322600	Weak transcription	Fetal Brain Female	brain
23	chr8:6304000-6338000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr8:6304400-6360200	Weak transcription	Esophagus	oesophagus
25	chr8:6304600-6321200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr8:6304800-6323000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr8:6305800-6322800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr8:6306200-6322800	Weak transcription	Fetal Intestine Large	intestine
29	chr8:6306200-6325400	Weak transcription	K562	blood
30	chr8:6306200-6328200	Weak transcription	Fetal Lung	lung
31	chr8:6306600-6322800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr8:6308000-6330000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr8:6308000-6338400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr8:6308000-6372600	Weak transcription	HMEC	breast
35	chr8:6312200-6338200	Weak transcription	Liver	Liver
36	chr8:6313200-6323200	Weak transcription	NHLF	lung
37	chr8:6313200-6338400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr8:6314200-6321600	Weak transcription	Lung	lung
39	chr8:6314400-6321400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr8:6314400-6322800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr8:6314400-6338200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr8:6314400-6339600	Weak transcription	Brain Angular Gyrus	brain
43	chr8:6314600-6321600	Weak transcription	GM12878-XiMat	blood
44	chr8:6314800-6322600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr8:6316400-6345600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr8:6317000-6321600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr8:6317600-6322800	Weak transcription	Fetal Intestine Small	intestine
48	chr8:6317600-6338400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr8:6317800-6321600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr8:6317800-6322200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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