Variant report

Variant	rs2440397
Chromosome Location	chr8:6328393-6328394
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:6327001..6332096-chr8:6332476..6335725,6	K562	blood:
2	chr8:6326969..6329620-chr8:6343917..6345900,2	K562	blood:

Variant related genes	Relation type
ENSG00000147316	Chromatin interaction

Extended variants
information (count: 159 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs1054073	0.94[JPT][hapmap]
rs1054074	0.83[ASN][1000 genomes]
rs11137029	1.00[CEU][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11137033	0.94[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1129703	0.87[JPT][hapmap]
rs1129704	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1129706	0.94[JPT][hapmap]
rs12545613	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12546890	0.82[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs12550299	1.00[CEU][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12674488	0.82[JPT][hapmap]
rs12675930	0.94[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12676907	0.94[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12676922	0.94[CEU][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12677501	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12679619	0.88[JPT][hapmap]
rs12680048	0.88[ASN][1000 genomes]
rs12681195	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13248420	0.82[JPT][hapmap]
rs13267816	0.92[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs13281967	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs13282022	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs13282577	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs1373307	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1530408	0.84[JPT][hapmap]
rs1530409	0.84[JPT][hapmap]
rs1550690	0.80[JPT][hapmap]
rs17077031	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17077056	0.94[CEU][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes]
rs17077067	0.94[CEU][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes]
rs17077083	0.88[JPT][hapmap];0.88[EUR][1000 genomes]
rs17077094	0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs17077109	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs17613024	0.82[CEU][hapmap];0.88[JPT][hapmap]
rs1867385	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1867386	0.94[JPT][hapmap]
rs1868551	0.94[JPT][hapmap]
rs1868555	0.80[ASN][1000 genomes]
rs2034143	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2251956	0.88[JPT][hapmap]
rs2254903	0.88[JPT][hapmap]
rs2277136	0.82[CEU][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes]
rs2440395	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2440396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440399	0.89[CEU][hapmap]
rs2440403	0.90[ASN][1000 genomes]
rs2440406	0.82[JPT][hapmap]
rs2440408	0.88[ASN][1000 genomes]
rs2440411	0.83[ASN][1000 genomes]
rs2440412	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2440413	0.82[JPT][hapmap]
rs2440414	0.94[JPT][hapmap]
rs2440415	0.83[ASN][1000 genomes]
rs2440416	0.88[JPT][hapmap]
rs2440419	0.81[ASN][1000 genomes]
rs2440422	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs2440423	0.88[JPT][hapmap]
rs2440424	0.88[JPT][hapmap]
rs2440427	0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2440428	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2440430	0.92[CHB][hapmap]
rs2440432	0.82[JPT][hapmap]
rs2442483	0.81[ASN][1000 genomes]
rs2442485	0.82[JPT][hapmap]
rs2442490	0.89[CEU][hapmap]
rs2442491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2442492	0.89[CEU][hapmap]
rs2442493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2442496	0.89[CEU][hapmap]
rs2442497	1.00[CEU][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2442499	0.88[ASN][1000 genomes]
rs2442500	0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2442502	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2442503	0.87[ASN][1000 genomes]
rs2442510	0.94[JPT][hapmap]
rs2442511	0.88[JPT][hapmap]
rs2442514	0.82[JPT][hapmap]
rs2442516	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs2442517	0.94[JPT][hapmap]
rs2442518	0.88[JPT][hapmap]
rs2442521	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2442522	0.88[JPT][hapmap]
rs2442523	0.89[JPT][hapmap]
rs2442524	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2442533	0.84[JPT][hapmap]
rs2515564	0.81[JPT][hapmap]
rs2515568	0.83[ASN][1000 genomes]
rs2515572	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2515573	0.83[ASN][1000 genomes]
rs2515574	0.92[CHB][hapmap]
rs2515576	0.87[ASN][1000 genomes]
rs2515585	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2916740	0.94[JPT][hapmap]
rs2916741	0.94[JPT][hapmap]
rs2916742	0.94[JPT][hapmap]
rs2916743	0.94[JPT][hapmap]
rs2916746	0.94[JPT][hapmap]
rs2916750	0.94[JPT][hapmap]
rs2920659	1.00[JPT][hapmap]
rs2920660	0.94[JPT][hapmap]
rs2920665	0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2920671	0.94[JPT][hapmap]
rs2920674	0.92[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2920677	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2920678	0.81[ASN][1000 genomes]
rs2920681	0.94[CEU][hapmap];0.82[JPT][hapmap]
rs2920689	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2922811	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2922813	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2922814	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2922815	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs2922818	0.94[JPT][hapmap]
rs2922820	0.94[JPT][hapmap]
rs2922821	0.86[ASN][1000 genomes]
rs2979648	1.00[JPT][hapmap]
rs2979652	0.94[JPT][hapmap]
rs2979655	0.89[CEU][hapmap]
rs2979664	0.81[ASN][1000 genomes]
rs3020270	0.94[JPT][hapmap]
rs34009442	0.88[ASN][1000 genomes]
rs34635086	0.88[ASN][1000 genomes]
rs56073811	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57804372	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58679306	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59635757	0.95[EUR][1000 genomes]
rs60915478	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6559160	0.84[JPT][hapmap]
rs6559161	0.82[JPT][hapmap]
rs6559162	0.82[JPT][hapmap]
rs6559164	0.82[JPT][hapmap]
rs6989935	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7001056	0.89[ASN][1000 genomes]
rs7002187	0.88[JPT][hapmap]
rs7002495	0.84[JPT][hapmap]
rs7002509	0.80[JPT][hapmap]
rs73196802	0.95[EUR][1000 genomes]
rs73520657	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73661775	0.88[EUR][1000 genomes]
rs7824209	0.94[JPT][hapmap]
rs7833479	0.88[EUR][1000 genomes]
rs7833481	1.00[CEU][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7833484	0.88[EUR][1000 genomes]
rs894888	0.84[JPT][hapmap]
rs894895	0.93[JPT][hapmap]
rs930557	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs963754	0.89[JPT][hapmap];0.80[ASN][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
rs2440397	MCPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

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	chr8:6303000-6338200	Weak transcription	Gastric	stomach
6	chr8:6303000-6338200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr8:6303000-6338400	Weak transcription	Colonic Mucosa	Colon
8	chr8:6303000-6338400	Weak transcription	Right Ventricle	heart
9	chr8:6303000-6339400	Weak transcription	Placenta	Placenta
10	chr8:6303200-6339400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr8:6303200-6339400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr8:6303200-6340000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr8:6303800-6338400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr8:6304000-6338000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr8:6304400-6360200	Weak transcription	Esophagus	oesophagus
16	chr8:6308000-6330000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr8:6308000-6338400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr8:6308000-6372600	Weak transcription	HMEC	breast
19	chr8:6312200-6338200	Weak transcription	Liver	Liver
20	chr8:6313200-6338400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr8:6314400-6338200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr8:6314400-6339600	Weak transcription	Brain Angular Gyrus	brain
23	chr8:6316400-6345600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr8:6317600-6338400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr8:6317800-6380200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr8:6318000-6338200	Weak transcription	Adipose Nuclei	Adipose
27	chr8:6318400-6339600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr8:6318600-6339600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr8:6318800-6334800	Weak transcription	NHDF-Ad	bronchial
30	chr8:6318800-6338400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr8:6319600-6338200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr8:6320600-6328800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr8:6321400-6334600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr8:6321400-6334600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr8:6321600-6339000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr8:6321800-6334600	Weak transcription	NH-A	brain
37	chr8:6321800-6338200	Weak transcription	Brain Substantia Nigra	brain
38	chr8:6321800-6338400	Weak transcription	Brain Anterior Caudate	brain
39	chr8:6321800-6342000	Weak transcription	Aorta	Aorta
40	chr8:6321800-6343800	Weak transcription	Hela-S3	cervix
41	chr8:6322000-6338200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr8:6322000-6340000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr8:6322000-6346800	Weak transcription	Colon Smooth Muscle	Colon
44	chr8:6322200-6332600	Weak transcription	Brain Hippocampus Middle	brain
45	chr8:6322200-6334600	Weak transcription	HSMM	muscle
46	chr8:6322200-6338200	Weak transcription	Left Ventricle	heart
47	chr8:6322200-6338200	Weak transcription	HSMMtube	muscle
48	chr8:6322200-6339800	Weak transcription	Psoas Muscle	Psoas
49	chr8:6322800-6334600	Weak transcription	HUVEC	blood vessel
50	chr8:6323000-6338400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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