Variant report

Variant	rs2302944
Chromosome Location	chr14:78390880-78390881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11159310	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12587141	0.86[CHD][hapmap];0.90[ASN][1000 genomes]
rs17753430	0.94[CEU][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes]
rs2287653	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];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4020127	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55748376	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7141888	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7145542	0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv565233	chr14:78366967-78390880	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv515961	chr14:78390880-78392008	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2302944	ALKBH1	cis	parietal	SCAN
rs2302944	PGF	cis	cerebellum	SCAN
rs2302944	COQ6	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78327800-78400600	Weak transcription	Colonic Mucosa	Colon
2	chr14:78349200-78397200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:78349200-78407200	Weak transcription	Colon Smooth Muscle	Colon
4	chr14:78352600-78398800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr14:78354800-78391600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr14:78355000-78391600	Weak transcription	Esophagus	oesophagus
7	chr14:78355600-78398000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr14:78356000-78393600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr14:78356000-78398600	Weak transcription	Fetal Intestine Large	intestine
10	chr14:78356800-78399600	Weak transcription	Thymus	Thymus
11	chr14:78357000-78398600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr14:78359200-78399600	Weak transcription	HSMMtube	muscle
13	chr14:78359200-78399800	Weak transcription	Primary B cells from cord blood	blood
14	chr14:78364000-78398800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr14:78366000-78393000	Weak transcription	Aorta	Aorta
16	chr14:78367400-78399200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr14:78369200-78392000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr14:78369400-78397400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr14:78369600-78394000	Weak transcription	Liver	Liver
20	chr14:78370000-78397600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr14:78372800-78399200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr14:78373000-78395200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr14:78374800-78391000	Weak transcription	Ovary	ovary
24	chr14:78375200-78391000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr14:78375200-78391600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr14:78375400-78400800	Weak transcription	NHEK	skin
27	chr14:78375600-78397800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr14:78376000-78392200	Weak transcription	Fetal Intestine Small	intestine
29	chr14:78377000-78392000	Weak transcription	Fetal Muscle Leg	muscle
30	chr14:78377000-78393200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr14:78377200-78398600	Weak transcription	Brain Substantia Nigra	brain
32	chr14:78377200-78399600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr14:78380000-78391000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr14:78381600-78399800	Weak transcription	Fetal Thymus	thymus
35	chr14:78384600-78392000	Weak transcription	Psoas Muscle	Psoas
36	chr14:78385000-78391000	Weak transcription	Brain Hippocampus Middle	brain
37	chr14:78385000-78391000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr14:78385000-78397800	Weak transcription	Left Ventricle	heart
39	chr14:78385000-78399600	Weak transcription	Brain Anterior Caudate	brain
40	chr14:78385000-78399600	Weak transcription	Dnd41	blood
41	chr14:78385000-78400000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr14:78385600-78391200	Weak transcription	Gastric	stomach
43	chr14:78387000-78397000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr14:78387200-78392400	Weak transcription	Adipose Nuclei	Adipose
45	chr14:78387400-78398000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr14:78387800-78391400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr14:78388600-78391400	Weak transcription	Fetal Stomach	stomach
48	chr14:78388800-78399400	Weak transcription	Brain Germinal Matrix	brain
49	chr14:78389000-78393400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr14:78389000-78398800	Weak transcription	Brain Inferior Temporal Lobe	brain

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