Variant report

Variant	rs2042864
Chromosome Location	chr3:141178979-141178980
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:141025929..141033510-chr3:141171081..141179408,10	MCF-7	breast:
2	chr3:141177832..141180375-chr3:141204869..141206491,3	K562	blood:
3	chr3:141177718..141181324-chr3:141593928..141596478,3	K562	blood:
4	chr3:141177945..141179663-chr3:141279624..141280925,17	K562	blood:
5	chr3:141178684..141179373-chr3:141276666..141277719,3	K562	blood:
6	chr3:141173421..141179159-chr3:141204636..141208201,13	MCF-7	breast:
7	chr3:141178686..141179587-chr3:141280024..141280748,3	MCF-7	breast:
8	chr3:141178968..141180548-chr3:141278934..141280564,2	K562	blood:
9	chr3:141178593..141179424-chr3:141278095..141278744,3	K562	blood:
10	chr3:141169710..141171431-chr3:141177334..141179161,2	K562	blood:
11	chr3:141178423..141179603-chr3:141279621..141280965,17	MCF-7	breast:
12	chr3:141178641..141179578-chr3:141631827..141632339,2	K562	blood:
13	chr3:141079392..141080078-chr3:141178700..141179365,3	K562	blood:
14	chr3:141177404..141179126-chr3:141193670..141195602,2	MCF-7	breast:
15	chr3:141025955..141033087-chr3:141172047..141179174,18	MCF-7	breast:
16	chr3:141169931..141172145-chr3:141175203..141179161,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000069849	Chromatin interaction
ENSG00000249540	Chromatin interaction
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11711375	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11917587	0.83[CEU][hapmap]
rs13069717	0.83[EUR][1000 genomes]
rs1366042	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1493209	0.96[CEU][hapmap]
rs1582875	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1863867	0.82[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2312193	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs295320	0.96[CEU][hapmap]
rs295323	0.92[CEU][hapmap];0.91[YRI][hapmap]
rs35711802	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3806646	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3821710	0.96[CEU][hapmap]
rs3821712	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6763498	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6767158	0.96[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6773734	0.95[ASN][1000 genomes]
rs6776003	0.82[CEU][hapmap]
rs6785874	0.96[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs6795168	0.96[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6800122	0.96[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6808837	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs7612543	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs7632308	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7643837	0.96[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9289630	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9289631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813177	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9851256	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs9878347	0.82[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs9879503	0.82[CEU][hapmap];0.91[YRI][hapmap];0.87[AFR][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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2042864	RASA2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141166600-141181600	Weak transcription	Pancreas	Pancrea
2	chr3:141166800-141179200	Weak transcription	Fetal Brain Male	brain
3	chr3:141168400-141179200	Weak transcription	Fetal Heart	heart
4	chr3:141168600-141181800	Weak transcription	Aorta	Aorta
5	chr3:141169000-141179000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:141171400-141179200	Weak transcription	Small Intestine	intestine
7	chr3:141171600-141179000	Weak transcription	Brain Anterior Caudate	brain
8	chr3:141174200-141179000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr3:141174200-141179000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:141174200-141179200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:141174200-141181000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:141174200-141182200	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:141174200-141182400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:141174200-141182400	Weak transcription	Brain Substantia Nigra	brain
15	chr3:141174800-141180800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:141176800-141183600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:141177000-141179200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:141177000-141179200	Weak transcription	A549	lung
19	chr3:141177000-141183800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:141177000-141184000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:141177000-141189600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:141177200-141179200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:141177600-141179400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:141178000-141179400	Enhancers	K562	blood
25	chr3:141178000-141184200	Weak transcription	NHLF	lung
26	chr3:141178000-141188200	Weak transcription	NHDF-Ad	bronchial
27	chr3:141178400-141181000	Weak transcription	HepG2	liver
28	chr3:141178600-141179600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:141178800-141179400	Enhancers	NH-A	brain
30	chr3:141178800-141179600	Enhancers	Osteobl	bone

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