Variant report

Variant	rs4838458
Chromosome Location	chr10:50348481-50348482
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50345704..50347282-chr10:50347596..50350389,2	K562	blood:
2	chr10:50341771..50344266-chr10:50346312..50348663,3	K562	blood:

Variant related genes	Relation type
ENSG00000172538	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10218854	0.82[CHB][hapmap]
rs11100995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11101001	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs11592975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11594275	0.96[ASN][1000 genomes]
rs11594452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11597983	1.00[ASN][1000 genomes]
rs11598768	0.96[ASN][1000 genomes]
rs12240840	0.93[EUR][1000 genomes]
rs12243520	0.96[ASN][1000 genomes]
rs17782866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1806681	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2246796	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2377981	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377982	0.94[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377983	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2377984	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3750744	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4073200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073201	0.96[ASN][1000 genomes]
rs4073202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41306832	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272720	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4284329	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4345884	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4603218	1.00[EUR][1000 genomes]
rs4838364	0.82[CHB][hapmap]
rs4838445	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs4838449	0.99[EUR][1000 genomes]
rs4838453	0.83[EUR][1000 genomes]
rs4838455	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838456	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4838460	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4838464	0.83[ASN][1000 genomes]
rs55687538	0.96[ASN][1000 genomes]
rs55783415	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55890352	0.96[ASN][1000 genomes]
rs56235933	0.97[EUR][1000 genomes]
rs56364323	0.96[ASN][1000 genomes]
rs56737365	0.93[ASN][1000 genomes]
rs57286767	0.96[ASN][1000 genomes]
rs59728475	0.96[ASN][1000 genomes]
rs61060205	0.96[ASN][1000 genomes]
rs61848451	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6537495	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs7080670	0.82[CHB][hapmap]
rs7081097	0.96[ASN][1000 genomes]
rs7088006	1.00[ASN][1000 genomes]
rs7094220	0.82[CHB][hapmap]
rs7094501	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7096516	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs7097375	0.96[ASN][1000 genomes]
rs73302715	0.93[ASN][1000 genomes]
rs73302716	0.93[ASN][1000 genomes]
rs73302780	1.00[ASN][1000 genomes]
rs73302786	0.96[ASN][1000 genomes]
rs7895212	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7924204	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9665275	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4838458	GDF2	cis	parietal	SCAN
rs4838458	CSTF2T	cis	parietal	SCAN
rs4838458	FRMPD2	cis	parietal	SCAN
rs4838458	SYT15	cis	cerebellum	SCAN
rs4838458	DDR2	trans	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50342200-50349800	Enhancers	Fetal Lung	lung
2	chr10:50343000-50357800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:50344200-50352200	Weak transcription	Fetal Thymus	thymus
4	chr10:50345600-50349600	Enhancers	Fetal Muscle Leg	muscle
5	chr10:50345800-50349000	Enhancers	Fetal Stomach	stomach
6	chr10:50345800-50349200	Enhancers	Fetal Muscle Trunk	muscle
7	chr10:50346200-50349000	Enhancers	Adipose Nuclei	Adipose
8	chr10:50346200-50349800	Enhancers	NHLF	lung
9	chr10:50346200-50354400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr10:50346400-50349600	Enhancers	Ovary	ovary
11	chr10:50346600-50348800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr10:50346600-50349600	Enhancers	HSMMtube	muscle
13	chr10:50346600-50350600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr10:50346800-50348800	Enhancers	Right Atrium	heart
15	chr10:50346800-50349000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr10:50346800-50349000	Enhancers	Left Ventricle	heart
17	chr10:50346800-50349000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr10:50346800-50349200	Enhancers	Placenta	Placenta
19	chr10:50346800-50351800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr10:50347000-50348800	Enhancers	Colonic Mucosa	Colon
21	chr10:50347000-50349000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr10:50347000-50349000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:50347000-50349800	Enhancers	K562	blood
24	chr10:50347600-50349000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr10:50347600-50349000	Enhancers	Right Ventricle	heart
26	chr10:50347800-50349000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr10:50347800-50349400	Enhancers	Osteobl	bone
28	chr10:50347800-50349800	Enhancers	NH-A	brain
29	chr10:50347800-50351200	Enhancers	NHDF-Ad	bronchial
30	chr10:50348000-50348600	Enhancers	HSMM	muscle
31	chr10:50348000-50348800	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr10:50348000-50349600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr10:50348000-50349800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr10:50348000-50351200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr10:50348000-50352200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr10:50348200-50348600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr10:50348400-50348600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr10:50348400-50349000	Enhancers	Spleen	Spleen

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