Variant report

Variant	rs2254863
Chromosome Location	chr10:50222585-50222586
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:50217414..50220289-chr10:50222557..50225109,2	K562	blood:
2	chr10:50221492..50223848-chr10:50223986..50225496,2	K562	blood:
3	chr10:50219903..50222688-chr10:50236599..50239408,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VSTM4-2	chr10:50222412-50224993	NONHSAT013287

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1055583	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1125517	0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs12763621	0.98[EUR][1000 genomes]
rs12763646	0.90[EUR][1000 genomes]
rs12764062	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs12764806	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs12765141	0.92[EUR][1000 genomes]
rs12767010	0.93[EUR][1000 genomes]
rs12768497	0.85[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs12769016	0.93[EUR][1000 genomes]
rs12770669	0.82[TSI][hapmap]
rs12770882	0.93[EUR][1000 genomes]
rs12774742	0.82[EUR][1000 genomes]
rs12775861	0.98[EUR][1000 genomes]
rs12775969	0.98[EUR][1000 genomes]
rs12779947	0.98[EUR][1000 genomes]
rs12782892	0.92[EUR][1000 genomes]
rs17773323	0.92[EUR][1000 genomes]
rs1877798	0.98[EUR][1000 genomes]
rs1877804	0.93[ASN][1000 genomes]
rs1877805	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs1877806	0.93[EUR][1000 genomes]
rs1913518	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1913519	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1913521	1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.93[ASN][1000 genomes]
rs1996185	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2102686	0.85[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs2137920	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2175916	0.99[EUR][1000 genomes]
rs2175917	0.99[EUR][1000 genomes]
rs2175918	0.82[ASW][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap]
rs2243994	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2244575	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs2244967	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2245145	0.92[ASN][1000 genomes]
rs2245147	0.92[ASN][1000 genomes]
rs2245149	0.92[ASN][1000 genomes]
rs2245162	0.92[ASN][1000 genomes]
rs2245165	0.89[ASN][1000 genomes]
rs2253873	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs2254384	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs2254393	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs2254410	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.82[YRI][hapmap];0.93[ASN][1000 genomes]
rs2254412	0.93[ASN][1000 genomes]
rs2254617	0.93[ASN][1000 genomes]
rs2254628	0.93[ASN][1000 genomes]
rs2254740	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs2254754	0.93[ASN][1000 genomes]
rs2255253	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255360	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2255739	0.94[ASN][1000 genomes]
rs2255943	0.93[ASN][1000 genomes]
rs2264555	0.93[ASN][1000 genomes]
rs2264844	0.93[ASN][1000 genomes]
rs2264848	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs2264849	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs2458672	0.93[ASN][1000 genomes]
rs2466751	0.93[ASN][1000 genomes]
rs2466752	0.93[ASN][1000 genomes]
rs2466754	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2466755	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2725199	0.94[ASN][1000 genomes]
rs2955063	0.92[ASN][1000 genomes]
rs34706288	0.98[EUR][1000 genomes]
rs3763776	0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs3810954	0.92[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7078453	0.98[EUR][1000 genomes]
rs7078724	0.98[EUR][1000 genomes]
rs7082251	0.98[EUR][1000 genomes]
rs7083453	0.99[EUR][1000 genomes]
rs7912598	0.82[TSI][hapmap]
rs883017	0.95[ASN][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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831866	chr10:50165180-50335276	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv6620	chr10:50197344-50224635	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2254863	ACAD11	trans	cerebellum	SCAN
rs2254863	MAPK8	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50210800-50223600	Weak transcription	Spleen	Spleen
2	chr10:50213400-50223000	Enhancers	Ovary	ovary
3	chr10:50216600-50223000	Enhancers	Placenta	Placenta
4	chr10:50217200-50226600	Weak transcription	Aorta	Aorta
5	chr10:50217400-50231200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr10:50217600-50227000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr10:50218600-50223800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr10:50218600-50225800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr10:50218600-50238200	Weak transcription	Esophagus	oesophagus
10	chr10:50218800-50231400	Weak transcription	Adipose Nuclei	Adipose
11	chr10:50219200-50226600	Weak transcription	HSMMtube	muscle
12	chr10:50220000-50225800	Weak transcription	Fetal Intestine Large	intestine
13	chr10:50220200-50222800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr10:50220400-50233600	Weak transcription	Gastric	stomach
15	chr10:50220600-50223000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr10:50220800-50223200	Enhancers	Fetal Stomach	stomach
17	chr10:50220800-50231200	Weak transcription	Brain Hippocampus Middle	brain
18	chr10:50221000-50223000	Enhancers	Fetal Lung	lung
19	chr10:50221000-50223600	Weak transcription	Fetal Muscle Leg	muscle
20	chr10:50221000-50233400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr10:50221400-50225200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr10:50221800-50222800	Enhancers	Duodenum Mucosa	Duodenum
23	chr10:50221800-50226600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr10:50221800-50227400	Weak transcription	Fetal Intestine Small	intestine
25	chr10:50221800-50231400	Weak transcription	Colon Smooth Muscle	Colon
26	chr10:50221800-50232400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr10:50222000-50231400	Weak transcription	Right Ventricle	heart
28	chr10:50222000-50233800	Weak transcription	Lung	lung
29	chr10:50222200-50223000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr10:50222200-50226600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr10:50222400-50222600	Enhancers	Small Intestine	intestine
32	chr10:50222400-50222800	Weak transcription	Left Ventricle	heart

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