Variant report

Variant	rs2879130
Chromosome Location	chr1:151830098-151830099
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151828500..151832022-chr1:151833324..151837098,3	K562	blood:
2	chr1:151637265..151639780-chr1:151828927..151831330,2	MCF-7	breast:
3	chr1:151803331..151805631-chr1:151828427..151830416,2	MCF-7	breast:
4	chr1:151822836..151827671-chr1:151828332..151832187,5	K562	blood:
5	chr1:151827756..151830746-chr1:151848383..151850324,3	MCF-7	breast:
6	chr1:151825580..151827671-chr1:151828953..151832187,3	K562	blood:
7	chr1:151818078..151821727-chr1:151829199..151833455,4	MCF-7	breast:
8	chr1:151821929..151826041-chr1:151829913..151833427,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143365	Chromatin interaction
ENSG00000196407	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1056037	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs1129117	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567049	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12727170	0.97[CHD][hapmap];0.82[GIH][hapmap];0.81[ASN][1000 genomes]
rs16833584	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16833599	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16833604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279503	0.81[CHB][hapmap];0.89[CHD][hapmap];0.84[ASN][1000 genomes]
rs4845624	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs60166269	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61815147	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6587625	0.95[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7524706	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7556386	0.86[CHB][hapmap];0.90[CHD][hapmap];0.85[ASN][1000 genomes]
rs923547	1.00[CEU][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs998500	0.82[ASN][1000 genomes]
rs998501	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]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2879130	NPR1	cis	parietal	SCAN
rs2879130	THEM4	cis	cerebellum	SCAN
rs2879130	S100A10	cis	lymphoblastoid	seeQTL
rs2879130	PLEKHO1	cis	cerebellum	SCAN
rs2879130	S100A10	cis	multi-tissue	Pritchard
rs2879130	LCE2C	cis	cerebellum	SCAN
rs2879130	THEM4	cis	parietal	SCAN
rs2879130	S100A10	cis	cerebellum	SCAN
rs2879130	C1orf230	cis	cerebellum	SCAN
rs2879130	SELENBP1	cis	parietal	SCAN
rs2879130	OTUD7B	cis	cerebellum	SCAN
rs2879130	S100A14	cis	cerebellum	SCAN
rs2879130	THEM4	cis	lymphoblastoid	seeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151819200-151847600	Weak transcription	Thymus	Thymus
2	chr1:151821000-151830600	Weak transcription	Right Atrium	heart
3	chr1:151821400-151832400	Weak transcription	Spleen	Spleen
4	chr1:151821600-151845600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:151826400-151846200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:151827600-151839800	Weak transcription	Hela-S3	cervix
7	chr1:151828200-151835400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:151828600-151830800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:151828800-151830200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:151828800-151830800	Weak transcription	Osteobl	bone
11	chr1:151828800-151837000	Weak transcription	Right Ventricle	heart
12	chr1:151829000-151830200	Weak transcription	Adipose Nuclei	Adipose
13	chr1:151829000-151830400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:151829000-151830600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:151829000-151845200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:151829200-151830600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:151829200-151830600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:151829200-151832000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:151829400-151834200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr1:151829800-151830400	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr1:151829800-151830600	Enhancers	Esophagus	oesophagus
22	chr1:151829800-151830600	Weak transcription	Placenta	Placenta
23	chr1:151829800-151830600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr1:151829800-151832800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:151829800-151832800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:151830000-151831000	Enhancers	Ovary	ovary
27	chr1:151830000-151833400	Enhancers	HMEC	breast
28	chr1:151830000-151833600	Enhancers	NHEK	skin
29	chr1:151830000-151833800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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