Variant report

Variant	rs2440415
Chromosome Location	chr8:6303859-6303860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1054073	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1054074	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1129703	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1129704	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1129706	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12545939	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1373306	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1373307	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530408	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1530409	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1867385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867386	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1868551	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1966818	0.83[EUR][1000 genomes]
rs1968585	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2034143	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053618	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2166006	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2251956	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2254903	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2440392	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2440396	0.82[ASN][1000 genomes]
rs2440397	0.83[ASN][1000 genomes]
rs2440403	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2440408	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2440411	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440412	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2440413	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2440414	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2440416	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2440419	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2440422	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2440423	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2440424	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2440427	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2442491	0.80[ASN][1000 genomes]
rs2442493	0.82[ASN][1000 genomes]
rs2442499	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2442500	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2442502	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2442503	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2442505	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2442506	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2442507	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2442510	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2442511	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2442512	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2442514	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2442515	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2442516	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2442517	0.83[ASN][1000 genomes]
rs2442518	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2442519	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2442520	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2442521	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2442522	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2442523	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442524	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2442527	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2442530	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2442533	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2515555	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2515564	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2515568	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2515570	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2515571	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2515572	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2515573	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2515574	0.82[ASN][1000 genomes]
rs2515576	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2515585	0.84[ASN][1000 genomes]
rs2916739	0.82[EUR][1000 genomes]
rs2916740	0.82[EUR][1000 genomes]
rs2916741	0.82[EUR][1000 genomes]
rs2916742	0.82[EUR][1000 genomes]
rs2916743	0.82[EUR][1000 genomes]
rs2916745	0.82[EUR][1000 genomes]
rs2916746	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2916750	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2920659	0.82[EUR][1000 genomes]
rs2920660	0.83[EUR][1000 genomes]
rs2920661	0.82[EUR][1000 genomes]
rs2920662	0.82[EUR][1000 genomes]
rs2920665	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2920666	0.88[EUR][1000 genomes]
rs2920668	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2920669	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2920671	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2922818	0.82[EUR][1000 genomes]
rs2922819	0.82[EUR][1000 genomes]
rs2922820	0.81[EUR][1000 genomes]
rs2922821	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2922822	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2922823	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2922824	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2922833	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2979647	0.92[EUR][1000 genomes]
rs2979648	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2979649	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2979650	0.91[EUR][1000 genomes]
rs2979652	0.82[EUR][1000 genomes]
rs3020275	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3020278	0.91[EUR][1000 genomes]
rs3816402	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57804372	0.82[ASN][1000 genomes]
rs6559161	0.89[EUR][1000 genomes]
rs6559162	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6989935	0.83[ASN][1000 genomes]
rs7001036	0.81[EUR][1000 genomes]
rs7001056	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7002187	0.85[EUR][1000 genomes]
rs7008037	0.82[EUR][1000 genomes]
rs7008227	0.82[EUR][1000 genomes]
rs7824209	0.82[EUR][1000 genomes]
rs894888	0.90[ASN][1000 genomes]
rs894895	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs930557	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs963754	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv1022940	chr8:6128828-6304814	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS 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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
rs2440415	MCPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr8:6278600-6305400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr8:6282800-6313400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr8:6287200-6309200	Weak transcription	Fetal Brain Male	brain
5	chr8:6287600-6306600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr8:6287600-6307600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr8:6287600-6344400	Weak transcription	Small Intestine	intestine
8	chr8:6287800-6304800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr8:6288400-6304400	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr8:6289000-6308000	Strong transcription	Dnd41	blood
11	chr8:6289200-6304000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr8:6289200-6306200	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr8:6289200-6306400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr8:6289400-6306600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr8:6290000-6305000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr8:6291800-6305800	Weak transcription	Stomach Mucosa	stomach
17	chr8:6294800-6304600	Strong transcription	Fetal Intestine Large	intestine
18	chr8:6295000-6305000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr8:6295000-6305000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr8:6297400-6304600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr8:6297400-6305000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr8:6297600-6305000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr8:6297800-6304800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr8:6297800-6305000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr8:6297800-6305200	Strong transcription	Fetal Muscle Leg	muscle
26	chr8:6297800-6306000	Strong transcription	Adipose Nuclei	Adipose
27	chr8:6297800-6306000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr8:6297800-6307600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr8:6298000-6307600	Strong transcription	GM12878-XiMat	blood
30	chr8:6298200-6304000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr8:6299000-6304800	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr8:6299000-6305200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr8:6299200-6304000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr8:6299200-6304200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr8:6299200-6308000	Strong transcription	Fetal Thymus	thymus
36	chr8:6299800-6304000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr8:6299800-6304400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr8:6299800-6304600	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr8:6300000-6304000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr8:6300000-6306200	Strong transcription	Primary T cells from cord blood	blood
41	chr8:6300000-6306200	Strong transcription	Fetal Lung	lung
42	chr8:6300200-6304800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr8:6300400-6304000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr8:6300800-6305800	Strong transcription	Brain Hippocampus Middle	brain
45	chr8:6301000-6309600	Weak transcription	Fetal Heart	heart
46	chr8:6301000-6338400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr8:6301400-6308800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr8:6301600-6304200	Weak transcription	NHLF	lung
49	chr8:6301600-6306200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr8:6302000-6304000	Strong transcription	Fetal Brain Female	brain

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