Variant report

Variant	rs2255938
Chromosome Location	chr5:89791258-89791259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89790586..89793384-chr5:89813145..89814868,2	K562	blood:
2	chr5:89769093..89771320-chr5:89790048..89793265,3	MCF-7	breast:
3	chr5:89787239..89791726-chr5:89792887..89795524,4	K562	blood:
4	chr5:89780327..89783012-chr5:89790179..89792320,2	K562	blood:
5	chr5:89770745..89773686-chr5:89789440..89792433,3	K562	blood:

Variant related genes	Relation type
ENSG00000113356	Chromatin interaction
ENSG00000176055	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs250372	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs250373	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs250374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs250375	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27198	0.82[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs27963	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4569906	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6877680	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs790081	0.81[TSI][hapmap]
rs812594	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	nsv882364	chr5:89748142-89808531	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2255938	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL
rs2255938	GPR98	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89771200-89796200	Weak transcription	Fetal Intestine Small	intestine
2	chr5:89771600-89798800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:89771600-89814400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:89773400-89795600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:89773600-89798800	Weak transcription	HMEC	breast
6	chr5:89773800-89816000	Weak transcription	HepG2	liver
7	chr5:89773800-89824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:89774000-89814600	Weak transcription	Dnd41	blood
9	chr5:89774400-89814600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:89776200-89799200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:89776200-89800400	Weak transcription	HUVEC	blood vessel
12	chr5:89776600-89798800	Weak transcription	NHEK	skin
13	chr5:89777000-89806600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:89780400-89799800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr5:89780400-89810800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:89780600-89822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:89780800-89800000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:89780800-89800400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:89781000-89799400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:89781200-89793600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:89783000-89800800	Weak transcription	A549	lung
22	chr5:89783800-89813400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:89784600-89795600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:89784800-89814600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr5:89785200-89798800	Weak transcription	NHDF-Ad	bronchial
26	chr5:89785400-89798800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:89785400-89799400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr5:89785400-89814600	Weak transcription	NHLF	lung
29	chr5:89786200-89799400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:89788800-89799800	Weak transcription	NH-A	brain
31	chr5:89789800-89798200	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr5:89790200-89794400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:89790200-89809600	Weak transcription	GM12878-XiMat	blood
34	chr5:89790400-89792000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:89791000-89791400	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr5:89791000-89791400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:89791200-89792200	Weak transcription	K562	blood

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