Variant report

Variant	rs248988
Chromosome Location	chr5:80437279-80437280
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs12659839	0.90[JPT][hapmap]
rs153229	0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs153230	0.85[ASN][1000 genomes]
rs153231	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs153232	0.85[ASN][1000 genomes]
rs153233	0.93[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs153234	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs153235	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs153236	0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs153237	0.88[ASN][1000 genomes]
rs153238	0.88[ASN][1000 genomes]
rs153239	0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs153240	0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs153241	0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs153242	0.87[ASN][1000 genomes]
rs153243	0.87[ASN][1000 genomes]
rs153244	0.87[ASN][1000 genomes]
rs168718	0.92[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs17213885	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs173596	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs190339	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs193786	0.94[ASN][1000 genomes]
rs2454870	0.87[ASN][1000 genomes]
rs248980	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs248981	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs248982	0.90[ASN][1000 genomes]
rs248983	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs248984	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs248985	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs248986	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs248987	0.97[ASN][1000 genomes]
rs248989	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248992	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs26889	0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs26890	0.87[ASN][1000 genomes]
rs26891	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs26892	0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs26893	0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs26894	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs26895	0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs26896	0.85[ASN][1000 genomes]
rs26898	0.86[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs27513	0.85[ASN][1000 genomes]
rs27558	0.87[ASN][1000 genomes]
rs27781	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs28820	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34115	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs34116	0.92[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs34117	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs34120	0.94[ASN][1000 genomes]
rs34121	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs34122	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs382926	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs40046	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs457365	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs466044	0.84[ASN][1000 genomes]
rs58200570	0.83[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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv830360	chr5:80283278-80446040	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1025799	chr5:80436584-80485252	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs248988	ARSB	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80410600-80446600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:80414200-80438000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:80418400-80443800	Weak transcription	Brain Angular Gyrus	brain
4	chr5:80419400-80438200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr5:80421800-80443600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr5:80422000-80443400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:80423000-80451400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr5:80423400-80443800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:80424400-80443800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:80424400-80445000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:80426400-80443800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr5:80429200-80443800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr5:80431600-80438800	Strong transcription	Primary T cells from cord blood	blood
14	chr5:80432800-80443800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:80434600-80442200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr5:80435800-80437400	Enhancers	Brain Substantia Nigra	brain
17	chr5:80435800-80438800	Enhancers	Fetal Muscle Leg	muscle
18	chr5:80436000-80438000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:80436200-80437400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:80436200-80437400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:80436200-80437400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:80436200-80437400	Enhancers	Colon Smooth Muscle	Colon
23	chr5:80436200-80437400	Enhancers	Ovary	ovary
24	chr5:80436200-80437400	Enhancers	NHLF	lung
25	chr5:80436200-80437800	Enhancers	Brain Germinal Matrix	brain
26	chr5:80436200-80438200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr5:80436200-80438600	Enhancers	Brain Hippocampus Middle	brain
28	chr5:80436200-80438800	Enhancers	Fetal Stomach	stomach
29	chr5:80436200-80442800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr5:80436400-80437400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:80436400-80437400	Enhancers	Rectal Smooth Muscle	rectum
32	chr5:80436400-80437400	Enhancers	Right Ventricle	heart
33	chr5:80436600-80438000	Weak transcription	Fetal Brain Female	brain
34	chr5:80436600-80443400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr5:80436800-80437600	Enhancers	Adipose Nuclei	Adipose
36	chr5:80436800-80438400	Enhancers	Fetal Heart	heart
37	chr5:80436800-80438600	Enhancers	Fetal Lung	lung
38	chr5:80436800-80440600	Weak transcription	Psoas Muscle	Psoas
39	chr5:80436800-80441200	Weak transcription	HepG2	liver
40	chr5:80436800-80441400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr5:80436800-80448600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:80437200-80438200	Weak transcription	Brain Anterior Caudate	brain
43	chr5:80437200-80440600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr5:80437200-80443800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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