Variant report

Variant	rs6776003
Chromosome Location	chr3:141266493-141266494
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11711375	0.89[CEU][hapmap];0.91[ASN][1000 genomes]
rs11916906	0.89[ASN][1000 genomes]
rs11917587	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13069717	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1366042	0.85[CEU][hapmap]
rs1493209	0.86[CEU][hapmap];0.91[ASN][1000 genomes]
rs1582875	0.83[CEU][hapmap]
rs1863867	0.81[ASN][1000 genomes]
rs2042864	0.82[CEU][hapmap]
rs2172471	0.87[ASN][1000 genomes]
rs2312193	0.82[CEU][hapmap]
rs2639998	0.87[ASN][1000 genomes]
rs295320	0.89[CEU][hapmap];0.88[ASN][1000 genomes]
rs295323	0.85[CEU][hapmap];0.88[ASN][1000 genomes]
rs35711802	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3806646	0.86[CEU][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3821710	0.89[CEU][hapmap];0.91[ASN][1000 genomes]
rs3821712	0.89[CEU][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440013	0.91[ASN][1000 genomes]
rs6440015	0.85[ASN][1000 genomes]
rs6763498	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6767158	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6785874	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6795168	0.86[CEU][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6800122	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6808837	0.89[CEU][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7632308	0.89[CEU][hapmap]
rs7643837	0.89[CEU][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9813177	0.89[CEU][hapmap];0.85[EUR][1000 genomes];0.96[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	nsv1006237	chr3:141227525-141300722	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1014365	chr3:141235379-141282615	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Red blood cell traits	23222517	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6776003	RASA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141229400-141267400	Weak transcription	Fetal Heart	heart
2	chr3:141236200-141281600	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:141236400-141276000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:141236400-141301000	Weak transcription	Brain Substantia Nigra	brain
5	chr3:141236400-141306600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:141236600-141275800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:141236600-141297000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:141236600-141299400	Weak transcription	Gastric	stomach
9	chr3:141237000-141299400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:141242200-141274800	Weak transcription	Lung	lung
11	chr3:141243400-141299400	Weak transcription	Spleen	Spleen
12	chr3:141246000-141278400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:141249200-141274600	Weak transcription	Liver	Liver
14	chr3:141254600-141270800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr3:141254600-141294400	Weak transcription	Esophagus	oesophagus
16	chr3:141254800-141266600	Weak transcription	K562	blood
17	chr3:141254800-141266800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:141254800-141269000	Weak transcription	Brain Angular Gyrus	brain
19	chr3:141254800-141274000	Weak transcription	HepG2	liver
20	chr3:141254800-141274600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:141254800-141275000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:141254800-141291400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:141254800-141292200	Weak transcription	Left Ventricle	heart
24	chr3:141254800-141295200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:141254800-141299200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:141254800-141299400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:141254800-141299400	Weak transcription	Right Ventricle	heart
28	chr3:141254800-141319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:141255000-141274600	Weak transcription	Placenta	Placenta
30	chr3:141255200-141304800	Weak transcription	Ovary	ovary
31	chr3:141255200-141320000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:141255400-141277200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:141255400-141319200	Weak transcription	Aorta	Aorta
34	chr3:141257000-141300200	Weak transcription	Pancreas	Pancrea
35	chr3:141258600-141275000	Weak transcription	HMEC	breast
36	chr3:141260000-141276600	Weak transcription	Hela-S3	cervix
37	chr3:141260800-141276400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:141261000-141269800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:141261000-141270200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:141261400-141278600	Weak transcription	NHLF	lung
41	chr3:141262000-141266600	Strong transcription	Osteobl	bone
42	chr3:141262400-141270200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr3:141262600-141266600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:141262600-141267200	Weak transcription	HSMM	muscle
45	chr3:141262600-141278800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:141263000-141271200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:141263200-141268000	Weak transcription	HSMMtube	muscle
48	chr3:141263600-141292000	Weak transcription	Colonic Mucosa	Colon
49	chr3:141263800-141288800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:141264000-141266600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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