Variant report

Variant	rs2287653
Chromosome Location	chr14:78397627-78397628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:78396385..78399196-chr14:78423059..78425223,2	K562	blood:
2	chr14:78395022..78397820-chr14:78443504..78445248,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11159310	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12587141	0.83[CHB][hapmap];0.86[CHD][hapmap];0.90[ASN][1000 genomes]
rs17753430	0.94[CEU][hapmap];0.82[TSI][hapmap]
rs2302944	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3783954	0.97[ASN][1000 genomes]
rs3783955	0.97[ASN][1000 genomes]
rs4020126	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4020127	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55748376	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7141888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7145542	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34345	chr14:78370455-78496587	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv2757576	chr14:78379156-78502019	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv2759999	chr14:78379156-78502019	Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv456345	chr14:78380390-78398891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv565234	chr14:78380390-78398891	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2287653	ALKBH1	cis	parietal	SCAN
rs2287653	PGF	cis	cerebellum	SCAN
rs2287653	COQ6	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78327800-78400600	Weak transcription	Colonic Mucosa	Colon
2	chr14:78349200-78407200	Weak transcription	Colon Smooth Muscle	Colon
3	chr14:78352600-78398800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr14:78355600-78398000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr14:78356000-78398600	Weak transcription	Fetal Intestine Large	intestine
6	chr14:78356800-78399600	Weak transcription	Thymus	Thymus
7	chr14:78357000-78398600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr14:78359200-78399600	Weak transcription	HSMMtube	muscle
9	chr14:78359200-78399800	Weak transcription	Primary B cells from cord blood	blood
10	chr14:78364000-78398800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr14:78367400-78399200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr14:78372800-78399200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr14:78375400-78400800	Weak transcription	NHEK	skin
14	chr14:78375600-78397800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr14:78377200-78398600	Weak transcription	Brain Substantia Nigra	brain
16	chr14:78377200-78399600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr14:78381600-78399800	Weak transcription	Fetal Thymus	thymus
18	chr14:78385000-78397800	Weak transcription	Left Ventricle	heart
19	chr14:78385000-78399600	Weak transcription	Brain Anterior Caudate	brain
20	chr14:78385000-78399600	Weak transcription	Dnd41	blood
21	chr14:78385000-78400000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr14:78387400-78398000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr14:78388800-78399400	Weak transcription	Brain Germinal Matrix	brain
24	chr14:78389000-78398800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr14:78389600-78399600	Weak transcription	Fetal Brain Female	brain
26	chr14:78389800-78399600	Weak transcription	Placenta	Placenta
27	chr14:78390400-78399400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr14:78390600-78398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr14:78391200-78400000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr14:78391400-78399800	Weak transcription	HepG2	liver
31	chr14:78391600-78399800	Weak transcription	Brain Angular Gyrus	brain
32	chr14:78391800-78398800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr14:78392200-78399600	Weak transcription	Psoas Muscle	Psoas
34	chr14:78392400-78398400	Weak transcription	Fetal Muscle Leg	muscle
35	chr14:78392600-78399600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr14:78393600-78397800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr14:78393600-78397800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr14:78394200-78398000	Weak transcription	Esophagus	oesophagus
39	chr14:78394200-78398800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr14:78394200-78399000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr14:78394200-78399400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr14:78394400-78398600	Weak transcription	Brain Hippocampus Middle	brain
43	chr14:78394400-78398600	Weak transcription	Fetal Stomach	stomach
44	chr14:78394400-78399400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr14:78394400-78399800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr14:78394400-78400200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr14:78394600-78398000	Weak transcription	Liver	Liver
48	chr14:78395200-78402200	Strong transcription	Primary T cells from cord blood	blood
49	chr14:78395400-78398000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr14:78395400-78401000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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