Variant report

Variant	rs12590199
Chromosome Location	chr14:78370455-78370456
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11159294	0.84[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs11159298	0.81[CEU][hapmap]
rs11159299	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11159300	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11159301	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11159302	0.80[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11159303	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11159305	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11159307	0.85[CHB][hapmap]
rs11621642	0.85[AMR][1000 genomes]
rs11622297	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11625833	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11626480	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11629157	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12587361	0.92[CEU][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12879726	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs12879890	0.83[AMR][1000 genomes]
rs12884153	0.84[CEU][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes]
rs12891444	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12897885	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17826188	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2003600	0.84[CEU][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes]
rs2013130	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2080817	0.80[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2080818	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2098584	0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2287650	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2364743	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2364842	0.84[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes]
rs2886166	0.83[AMR][1000 genomes]
rs3783962	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3783966	0.92[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3783968	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3783969	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3783970	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3783972	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4359362	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs4393507	0.84[CEU][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes]
rs4411442	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4903654	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs4903656	0.92[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4903657	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4903658	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4903663	0.80[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4903666	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4903667	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7145567	0.89[CEU][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes]
rs7147735	0.89[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7149884	0.80[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs719049	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs726538	0.80[ASW][hapmap];0.84[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes]
rs734654	0.92[CEU][hapmap];0.95[GIH][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs741573	0.92[CEU][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs741574	0.89[ASW][hapmap];0.92[CEU][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7493235	0.84[AMR][1000 genomes]
rs7494718	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8014296	0.81[CEU][hapmap]
rs8020016	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs877561	0.92[CEU][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs962540	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043788	chr14:78178490-78381190	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12590199	FCF1	cis	parietal	SCAN
rs12590199	RPS6KL1	cis	cerebellum	SCAN
rs12590199	ADCK1	cis	lymphoblastoid	seeQTL
rs12590199	ADCK1	cis	multi-tissue	Pritchard

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78327800-78400600	Weak transcription	Colonic Mucosa	Colon
2	chr14:78346600-78375600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr14:78349200-78397200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr14:78349200-78407200	Weak transcription	Colon Smooth Muscle	Colon
5	chr14:78349400-78378000	Weak transcription	Fetal Brain Female	brain
6	chr14:78350800-78375800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr14:78350800-78376200	Weak transcription	Brain Angular Gyrus	brain
8	chr14:78352600-78398800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr14:78354000-78375800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr14:78354000-78375800	Weak transcription	Gastric	stomach
11	chr14:78354400-78374400	Weak transcription	Fetal Muscle Leg	muscle
12	chr14:78354600-78375800	Weak transcription	Brain Substantia Nigra	brain
13	chr14:78354800-78379200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr14:78354800-78391600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr14:78355000-78374000	Weak transcription	Ovary	ovary
16	chr14:78355000-78375400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr14:78355000-78390800	Weak transcription	Spleen	Spleen
18	chr14:78355000-78391600	Weak transcription	Esophagus	oesophagus
19	chr14:78355200-78375000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr14:78355400-78370600	Weak transcription	Dnd41	blood
21	chr14:78355600-78398000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr14:78356000-78393600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr14:78356000-78398600	Weak transcription	Fetal Intestine Large	intestine
24	chr14:78356200-78390800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr14:78356800-78373800	Weak transcription	Fetal Intestine Small	intestine
26	chr14:78356800-78373800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr14:78356800-78399600	Weak transcription	Thymus	Thymus
28	chr14:78357000-78398600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr14:78358200-78373800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr14:78359200-78399600	Weak transcription	HSMMtube	muscle
31	chr14:78359200-78399800	Weak transcription	Primary B cells from cord blood	blood
32	chr14:78359400-78384200	Weak transcription	Right Ventricle	heart
33	chr14:78359800-78390800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr14:78360000-78373800	Weak transcription	Lung	lung
35	chr14:78360600-78378800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr14:78360600-78379200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr14:78364000-78398800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr14:78364200-78375400	Weak transcription	Osteobl	bone
39	chr14:78365200-78371000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr14:78366000-78372000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr14:78366000-78372000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr14:78366000-78375800	Weak transcription	Brain Anterior Caudate	brain
43	chr14:78366000-78376000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr14:78366000-78376200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr14:78366000-78393000	Weak transcription	Aorta	Aorta
46	chr14:78366400-78379200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr14:78366600-78374200	Weak transcription	Pancreas	Pancrea
48	chr14:78367400-78374200	Weak transcription	Fetal Stomach	stomach
49	chr14:78367400-78399200	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr14:78369000-78374400	Weak transcription	Adipose Nuclei	Adipose

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