Variant report

Variant	rs998501
Chromosome Location	chr1:151825572-151825573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151825281..151825782-chr3:73045773..73046421,2	HCT-116	colon:
2	chr1:151825263..151825781-chr3:73045429..73046269,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OAZ3-2	chr1:151822709-151826517	NONHSAT006440
2	lnc-OAZ3-2	chr1:151822709-151826136	NONHSAT006442

Variant related genes	Relation type
ENSG00000163605	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1056037	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs1129117	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12567049	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16833584	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16833599	0.89[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16833604	1.00[CEU][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279503	0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[ASN][1000 genomes]
rs2879130	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845624	0.86[CHB][hapmap]
rs60166269	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61815147	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6587625	0.95[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7524706	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7556386	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs923547	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs998500	0.81[ASN][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	esv1804657	chr1:151784152-151825756	Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1008033	chr1:151785029-151843154	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs998501	S100A10	cis	cerebellum	SCAN
rs998501	PLEKHO1	cis	cerebellum	SCAN
rs998501	THEM4	cis	lymphoblastoid	seeQTL
rs998501	C1orf230	cis	cerebellum	SCAN
rs998501	S100A14	cis	cerebellum	SCAN
rs998501	S100A10	cis	lymphoblastoid	seeQTL
rs998501	LCE2C	cis	cerebellum	SCAN
rs998501	NPR1	cis	parietal	SCAN
rs998501	OTUD7B	cis	cerebellum	SCAN
rs998501	THEM4	cis	cerebellum	SCAN
rs998501	THEM4	cis	parietal	SCAN
rs998501	SELENBP1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151813400-151828600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:151814800-151827400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:151819200-151827200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:151819200-151847600	Weak transcription	Thymus	Thymus
5	chr1:151820000-151825800	Weak transcription	Hela-S3	cervix
6	chr1:151820600-151827200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:151821000-151830600	Weak transcription	Right Atrium	heart
8	chr1:151821400-151832400	Weak transcription	Spleen	Spleen
9	chr1:151821600-151845600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:151824000-151827800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:151824400-151826400	Enhancers	Placenta	Placenta
12	chr1:151824400-151826600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:151824400-151828200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:151824600-151827800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:151824800-151826000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:151824800-151828400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:151825200-151825800	Weak transcription	Esophagus	oesophagus
18	chr1:151825200-151826600	Weak transcription	Right Ventricle	heart
19	chr1:151825400-151825600	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:151825400-151825800	Weak transcription	Gastric	stomach

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