Variant report

Variant	rs2442536
Chromosome Location	chr8:6276063-6276064
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:6275765..6277346-chr8:6279948..6281566,2	K562	blood:
2	chr8:6274685..6276639-chr8:6565162..6567770,2	MCF-7	breast:
3	chr8:6264019..6265631-chr8:6276024..6277548,2	K562	blood:

Variant related genes	Relation type
ENSG00000147316	Chromatin interaction
ENSG00000155189	Chromatin interaction
ENSG00000249898	Chromatin interaction
ENSG00000246089	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10103862	0.84[YRI][hapmap]
rs10104726	0.84[YRI][hapmap]
rs1057187	0.82[YRI][hapmap]
rs11137033	0.85[JPT][hapmap]
rs1129704	0.82[CHB][hapmap]
rs12674488	0.84[JPT][hapmap]
rs12677501	0.84[JPT][hapmap]
rs1530408	0.90[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1530409	0.86[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1550697	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1550698	0.98[EUR][1000 genomes]
rs17076812	0.81[CEU][hapmap]
rs17077109	0.84[JPT][hapmap]
rs1867385	0.81[CHB][hapmap];0.96[YRI][hapmap]
rs1966818	0.86[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs1968585	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2034143	0.81[CHB][hapmap]
rs2120483	0.98[EUR][1000 genomes]
rs2243755	0.82[YRI][hapmap]
rs2305022	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2440392	0.88[YRI][hapmap]
rs2440399	0.91[YRI][hapmap]
rs2440401	0.92[YRI][hapmap]
rs2440412	0.82[CHB][hapmap]
rs2440413	0.82[CHB][hapmap]
rs2440422	0.88[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap]
rs2440427	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2440428	0.84[JPT][hapmap]
rs2440443	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2440448	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2440452	0.91[YRI][hapmap]
rs2442490	0.88[YRI][hapmap]
rs2442491	0.82[JPT][hapmap]
rs2442492	0.87[YRI][hapmap]
rs2442496	0.91[YRI][hapmap]
rs2442500	0.90[YRI][hapmap]
rs2442502	0.83[YRI][hapmap]
rs2442516	0.88[CHB][hapmap];0.85[JPT][hapmap];0.91[YRI][hapmap]
rs2442517	0.84[JPT][hapmap];0.91[YRI][hapmap]
rs2442518	0.83[YRI][hapmap]
rs2442521	0.81[JPT][hapmap];0.81[AFR][1000 genomes]
rs2442522	0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2442523	0.88[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs2442524	0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs2442527	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2442530	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2442533	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2442546	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2515485	0.82[YRI][hapmap]
rs2515491	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2515555	0.91[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2515564	0.89[JPT][hapmap]
rs2515565	0.90[JPT][hapmap];0.96[YRI][hapmap]
rs2515572	0.81[CHB][hapmap]
rs2515582	0.80[YRI][hapmap]
rs2515583	0.92[YRI][hapmap]
rs2920656	0.87[YRI][hapmap]
rs2920665	0.85[JPT][hapmap]
rs2920677	0.83[JPT][hapmap];0.85[YRI][hapmap]
rs2920689	0.84[JPT][hapmap];0.87[YRI][hapmap]
rs2922813	0.87[YRI][hapmap]
rs2922814	0.84[JPT][hapmap];0.82[YRI][hapmap]
rs2922815	0.88[YRI][hapmap]
rs2979656	0.88[YRI][hapmap]
rs60526807	0.98[EUR][1000 genomes]
rs61048567	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6559160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6559161	0.85[JPT][hapmap]
rs6994734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs6995735	1.00[CEU][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs7002495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7002509	0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7008037	0.90[CEU][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs7008227	0.86[CEU][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs7009134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs725438	0.81[YRI][hapmap]
rs894888	0.81[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs930557	0.82[CHB][hapmap]
rs963754	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs9692902	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 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	nsv1018782	chr8:5984032-6284373	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	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
5	nsv949501	chr8:6081704-6303511	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv1024103	chr8:6124125-6303511	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1026950	chr8:6127991-6303511	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1025734	chr8:6128828-6303511	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	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
12	nsv527005	chr8:6129051-6287170	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1028552	chr8:6129221-6303511	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1021800	chr8:6144798-6286635	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	nsv1018882	chr8:6204857-6289937	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	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
21	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
22	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
23	nsv524404	chr8:6263083-6291485	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
24	nsv1030323	chr8:6268228-6279511	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2442536	MCPH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6265000-6286600	Weak transcription	Small Intestine	intestine
2	chr8:6265000-6339200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr8:6265200-6281800	Weak transcription	Right Atrium	heart
4	chr8:6265200-6281800	Weak transcription	Right Ventricle	heart
5	chr8:6265200-6282600	Weak transcription	Colonic Mucosa	Colon
6	chr8:6265200-6302200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr8:6265400-6278200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr8:6265400-6287400	Weak transcription	Psoas Muscle	Psoas
9	chr8:6265400-6303800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:6265600-6276400	Weak transcription	Fetal Brain Male	brain
11	chr8:6265600-6290000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr8:6267600-6291400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr8:6267600-6302400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr8:6268200-6282800	Weak transcription	NHLF	lung
15	chr8:6268200-6287400	Weak transcription	Colon Smooth Muscle	Colon
16	chr8:6268400-6282800	Weak transcription	Fetal Kidney	kidney
17	chr8:6268800-6291600	Weak transcription	HSMMtube	muscle
18	chr8:6269000-6278200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr8:6269400-6281600	Weak transcription	Fetal Heart	heart
20	chr8:6269400-6281800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr8:6269600-6278800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr8:6269600-6280200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr8:6269600-6282800	Weak transcription	HSMM	muscle
24	chr8:6269800-6278000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr8:6269800-6281400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr8:6269800-6281600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr8:6269800-6281800	Weak transcription	NHDF-Ad	bronchial
28	chr8:6269800-6286600	Weak transcription	Pancreas	Pancrea
29	chr8:6269800-6286600	Weak transcription	Stomach Mucosa	stomach
30	chr8:6269800-6290200	Weak transcription	NH-A	brain
31	chr8:6270200-6277600	Weak transcription	Hela-S3	cervix
32	chr8:6270200-6278800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr8:6270200-6295000	Weak transcription	Fetal Brain Female	brain
34	chr8:6270600-6282600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr8:6270600-6283000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr8:6271000-6282600	Weak transcription	Brain Anterior Caudate	brain
37	chr8:6271200-6279600	Strong transcription	Fetal Stomach	stomach
38	chr8:6272000-6276200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr8:6272000-6277200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr8:6272000-6278400	Strong transcription	K562	blood
41	chr8:6272200-6276400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr8:6272200-6277200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr8:6272600-6279600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr8:6272800-6277800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr8:6272800-6278600	Weak transcription	HUVEC	blood vessel
46	chr8:6272800-6282400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr8:6273000-6277800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr8:6273000-6278200	Weak transcription	Fetal Lung	lung
49	chr8:6273000-6281800	Weak transcription	Left Ventricle	heart
50	chr8:6273000-6286600	Weak transcription	Ovary	ovary

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