Variant report

Variant	rs2438349
Chromosome Location	chr5:90052372-90052373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90050605..90053422-chr5:90072276..90073803,2	K562	blood:
2	chr5:90017738..90019291-chr5:90051268..90053042,2	K562	blood:
3	chr5:89989229..89992043-chr5:90052048..90054479,3	K562	blood:

Variant related genes	Relation type
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10062026	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10070074	0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1158530	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658034	0.91[JPT][hapmap]
rs12658994	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs1988093	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1996549	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2030272	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2222241	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2222243	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247747	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2366929	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2438337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2438347	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2438350	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2438356	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2438357	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2438359	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2438367	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2438371	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2438372	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2443060	0.88[ASN][1000 genomes]
rs2443061	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2443064	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2443065	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2443066	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2443067	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2460162	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460163	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2460164	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2460165	0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2460181	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2460185	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2460186	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460187	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2460188	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs990124	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv934323	chr5:89968158-90111853	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1031718	chr5:89999033-90099868	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2438349	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL
rs2438349	GPR98	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90022400-90074000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:90034600-90059600	Weak transcription	Brain Anterior Caudate	brain
3	chr5:90036200-90066000	Weak transcription	Pancreas	Pancrea
4	chr5:90036600-90059800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:90037200-90058600	Weak transcription	Fetal Brain Female	brain
6	chr5:90038200-90064400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:90039800-90082000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:90041800-90055200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:90042000-90053400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:90042800-90058600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:90043000-90062400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:90043600-90054200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:90043600-90086800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr5:90044200-90059600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:90045200-90065200	Weak transcription	Brain Germinal Matrix	brain
16	chr5:90045600-90073000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr5:90047400-90052600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:90047400-90060400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr5:90048400-90089200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr5:90048600-90068600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:90051000-90054000	Weak transcription	K562	blood
22	chr5:90051800-90105000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:90052200-90053000	Enhancers	Fetal Intestine Large	intestine
24	chr5:90052200-90054800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr5:90052200-90055600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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