Variant report

Variant	rs6587622
Chromosome Location	chr1:151814405-151814406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151811113..151814780-chr1:151962857..151966577,5	MCF-7	breast:
2	chr1:151774281..151778666-chr1:151812036..151815315,4	MCF-7	breast:
3	chr1:151797661..151799547-chr1:151812000..151814982,2	MCF-7	breast:
4	chr1:151812887..151815507-chr1:151862226..151864970,2	MCF-7	breast:
5	chr1:151737837..151739955-chr1:151812642..151814916,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OAZ3-2	chr1:151814353-151814507	ENSG00000234614.1
2	lnc-OAZ3-2	chr1:151814088-151814507	NONHSAT006440

No data

Variant related genes	Relation type
ENSG00000213171	Chromatin interaction
ENSG00000268288	Chromatin interaction
ENSG00000232937	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000143450	Chromatin interaction
ENSG00000143365	Chromatin interaction
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1056037	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10788810	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10888438	0.83[EUR][1000 genomes]
rs12029913	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12122596	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16833604	0.80[CHB][hapmap]
rs2130529	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2279503	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs6587625	0.81[CHB][hapmap]
rs6667460	0.83[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7524706	0.82[CHB][hapmap]
rs7551686	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7551806	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7556386	0.81[CHB][hapmap];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	nsv516369	chr1:151780177-151820324	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	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
3	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6587622	C1orf51	cis	cerebellum	SCAN
rs6587622	MRPS21	cis	cerebellum	SCAN
rs6587622	THEM4	cis	lymphoblastoid	seeQTL
rs6587622	PGLYRP3	cis	cerebellum	SCAN
rs6587622	LCE1F	cis	parietal	SCAN
rs6587622	S100A2	cis	cerebellum	SCAN
rs6587622	S100A10	cis	lymphoblastoid	seeQTL
rs6587622	HRNR	cis	cerebellum	SCAN
rs6587622	THEM4	cis	cerebellum	SCAN
rs6587622	PLEKHO1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151810000-151818800	Weak transcription	A549	lung
2	chr1:151812200-151814600	Enhancers	HUVEC	blood vessel
3	chr1:151812600-151814600	Enhancers	NH-A	brain
4	chr1:151812800-151820600	Weak transcription	Right Atrium	heart
5	chr1:151813000-151814600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:151813000-151814800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:151813200-151814600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:151813200-151814600	Enhancers	Osteobl	bone
9	chr1:151813200-151814800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:151813200-151818800	Weak transcription	Placenta	Placenta
11	chr1:151813200-151818800	Weak transcription	Gastric	stomach
12	chr1:151813200-151819000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:151813400-151815200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:151813400-151818400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:151813400-151818400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:151813400-151818600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:151813400-151818600	Weak transcription	Pancreas	Pancrea
18	chr1:151813400-151818800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:151813400-151819000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:151813400-151819000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:151813400-151821200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:151813400-151828600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:151813800-151818600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:151813800-151818600	Weak transcription	NHEK	skin
25	chr1:151814000-151818200	Weak transcription	Hela-S3	cervix
26	chr1:151814000-151819000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr1:151814000-151820800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:151814200-151816200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:151814200-151818600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:151814400-151818600	Weak transcription	HMEC	breast

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