Variant report

Variant	rs13424899
Chromosome Location	chr2:114472260-114472261
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114467029..114469645-chr2:114471402..114474213,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10169190	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197009	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208651	0.93[ASN][1000 genomes]
rs1062074	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11123202	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11123203	0.93[ASN][1000 genomes]
rs11677168	0.93[ASN][1000 genomes]
rs12329244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711781	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12711787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12986781	0.86[ASN][1000 genomes]
rs13003858	0.86[ASN][1000 genomes]
rs13025042	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13028979	0.93[ASN][1000 genomes]
rs13389017	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13393247	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13395272	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13401587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13407986	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13408264	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409879	0.87[EUR][1000 genomes]
rs13410586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416738	0.87[EUR][1000 genomes]
rs13417896	0.93[ASN][1000 genomes]
rs13428433	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17048297	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17048299	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17048352	0.82[LWK][hapmap]
rs17048506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17633451	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs28392566	0.84[EUR][1000 genomes]
rs34026450	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34451679	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34480436	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35049717	0.83[EUR][1000 genomes]
rs35073956	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35255260	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762491	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62158991	0.81[ASN][1000 genomes]
rs62170066	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722177	0.87[ASN][1000 genomes]
rs7589738	1.00[CHB][hapmap]
rs7600251	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs998151	0.84[EUR][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	nsv1001195	chr2:114362003-114506330	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv979109	chr2:114429638-114495192	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv979339	chr2:114430138-114495192	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1009509	chr2:114432965-114557306	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv535896	chr2:114432965-114557306	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers 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 miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13424899	MGC70863	trans	multi-tissue	Pritchard
rs13424899	CHCHD5	cis	cerebellum	SCAN
rs13424899	SLC35F5	cis	cerebellum	SCAN
rs13424899	SLC35F5	cis	parietal	SCAN
rs13424899	RPL23AP7	cis	multi-tissue	Pritchard
rs13424899	ACTR3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114458200-114486200	Weak transcription	Dnd41	blood
2	chr2:114458200-114512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:114458400-114475000	Weak transcription	Thymus	Thymus
4	chr2:114458400-114484200	Weak transcription	Pancreas	Pancrea
5	chr2:114458400-114497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr2:114458400-114500000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:114460200-114484200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:114460800-114475200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:114461000-114472600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:114461200-114473200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:114461400-114513200	Weak transcription	Small Intestine	intestine
12	chr2:114461600-114484200	Weak transcription	Lung	lung
13	chr2:114461600-114484400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:114461600-114499800	Weak transcription	Hela-S3	cervix
15	chr2:114461800-114472400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:114462000-114497400	Weak transcription	Colonic Mucosa	Colon
17	chr2:114463000-114498800	Weak transcription	Esophagus	oesophagus
18	chr2:114463800-114473000	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:114464000-114473800	Weak transcription	Brain Anterior Caudate	brain
20	chr2:114464000-114473800	Weak transcription	Psoas Muscle	Psoas
21	chr2:114464000-114484200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:114464000-114484200	Weak transcription	Gastric	stomach
23	chr2:114464000-114497600	Weak transcription	Right Ventricle	heart
24	chr2:114464000-114497600	Weak transcription	Spleen	Spleen
25	chr2:114464400-114473000	Weak transcription	Fetal Lung	lung
26	chr2:114464600-114484600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:114465200-114486400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:114465200-114512000	Weak transcription	Stomach Mucosa	stomach
29	chr2:114465800-114480000	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:114465800-114484800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:114466200-114473800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:114466800-114474600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:114466800-114475400	Weak transcription	Brain Germinal Matrix	brain
34	chr2:114467400-114479800	Weak transcription	Brain Angular Gyrus	brain
35	chr2:114467400-114497200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:114467600-114486200	Weak transcription	Fetal Brain Male	brain
37	chr2:114467800-114484200	Weak transcription	Aorta	Aorta
38	chr2:114468400-114475600	Weak transcription	Fetal Intestine Small	intestine
39	chr2:114468600-114474000	Weak transcription	Brain Substantia Nigra	brain
40	chr2:114468800-114512800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr2:114469000-114473800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:114469400-114473800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:114469400-114473800	Strong transcription	Osteobl	bone
44	chr2:114469400-114477200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:114469400-114477200	Strong transcription	Placenta	Placenta
46	chr2:114469400-114477400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:114469400-114510400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:114469600-114476800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr2:114469800-114482000	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr2:114469800-114486400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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