Variant report

Variant	rs13062809
Chromosome Location	chr3:141294871-141294872
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141000930..141002501-chr3:141293837..141295898,2	K562	blood:
2	chr3:141289820..141291967-chr3:141293825..141295688,2	MCF-7	breast:
3	chr3:141289287..141291021-chr3:141292681..141295308,2	MCF-7	breast:
4	chr3:141292412..141295097-chr3:141295843..141298423,3	K562	blood:

Variant related genes	Relation type
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11557453	0.93[ASN][1000 genomes]
rs11711375	0.88[EUR][1000 genomes]
rs11714208	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11717144	0.93[ASN][1000 genomes]
rs11916906	0.89[EUR][1000 genomes]
rs12695740	0.93[ASN][1000 genomes]
rs12695741	0.93[ASN][1000 genomes]
rs12695743	0.93[ASN][1000 genomes]
rs13067519	0.93[ASN][1000 genomes]
rs13069717	0.82[EUR][1000 genomes]
rs13095168	0.87[ASN][1000 genomes]
rs13099945	0.87[ASN][1000 genomes]
rs1493209	0.90[EUR][1000 genomes]
rs2172471	0.87[EUR][1000 genomes]
rs2312194	0.87[ASN][1000 genomes]
rs2639998	0.86[EUR][1000 genomes]
rs295320	0.88[EUR][1000 genomes]
rs295323	0.87[EUR][1000 genomes]
rs34342794	0.87[ASN][1000 genomes]
rs35711802	0.82[EUR][1000 genomes]
rs3806646	0.81[EUR][1000 genomes]
rs3821710	0.89[EUR][1000 genomes]
rs3821712	0.81[EUR][1000 genomes]
rs4334619	0.90[ASN][1000 genomes]
rs6440013	0.88[EUR][1000 genomes]
rs6440015	0.86[EUR][1000 genomes]
rs6763498	0.82[EUR][1000 genomes]
rs6767158	0.81[EUR][1000 genomes]
rs6785874	0.82[EUR][1000 genomes]
rs6795168	0.82[EUR][1000 genomes]
rs6800122	0.82[EUR][1000 genomes]
rs6808837	0.82[EUR][1000 genomes]
rs720663	0.87[ASN][1000 genomes]
rs7643837	0.82[EUR][1000 genomes]
rs9813177	0.82[EUR][1000 genomes]
rs9829588	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9833121	0.90[ASN][1000 genomes]
rs9836050	0.87[ASN][1000 genomes]
rs9836818	0.87[ASN][1000 genomes]
rs9838230	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9840159	0.93[ASN][1000 genomes]
rs9840697	0.87[ASN][1000 genomes]
rs9865971	0.87[ASN][1000 genomes]
rs9870749	0.90[ASN][1000 genomes]
rs9873042	0.93[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	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	esv1795799	chr3:141284383-141301451	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv1794809	chr3:141290177-141304631	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13062809	RASA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141236400-141301000	Weak transcription	Brain Substantia Nigra	brain
2	chr3:141236400-141306600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:141236600-141297000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:141236600-141299400	Weak transcription	Gastric	stomach
5	chr3:141237000-141299400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:141243400-141299400	Weak transcription	Spleen	Spleen
7	chr3:141254800-141295200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:141254800-141299200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:141254800-141299400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:141254800-141299400	Weak transcription	Right Ventricle	heart
11	chr3:141254800-141319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:141255200-141304800	Weak transcription	Ovary	ovary
13	chr3:141255200-141320000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:141255400-141319200	Weak transcription	Aorta	Aorta
15	chr3:141257000-141300200	Weak transcription	Pancreas	Pancrea
16	chr3:141265200-141336200	Weak transcription	Psoas Muscle	Psoas
17	chr3:141267400-141295000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:141268400-141297800	Weak transcription	Fetal Heart	heart
19	chr3:141271200-141299400	Weak transcription	Brain Angular Gyrus	brain
20	chr3:141272600-141319200	Strong transcription	Dnd41	blood
21	chr3:141275800-141320600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:141276000-141299400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:141276200-141297000	Weak transcription	Lung	lung
24	chr3:141276400-141329400	Weak transcription	Small Intestine	intestine
25	chr3:141277200-141297000	Weak transcription	Thymus	Thymus
26	chr3:141277200-141341400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:141277600-141296400	Weak transcription	Hela-S3	cervix
28	chr3:141277800-141312000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr3:141278000-141296800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:141281800-141297000	Weak transcription	Fetal Intestine Small	intestine
31	chr3:141281800-141329400	Weak transcription	Fetal Brain Male	brain
32	chr3:141283400-141295000	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:141284600-141299200	Weak transcription	Fetal Stomach	stomach
34	chr3:141288000-141312400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:141288200-141295200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:141288200-141320000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:141288400-141295200	Strong transcription	Primary B cells from cord blood	blood
38	chr3:141288400-141316400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr3:141288600-141295000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:141288600-141295000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:141288600-141295400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:141288600-141302800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:141288600-141308400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:141288600-141316400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr3:141288800-141299800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:141289000-141311800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:141289000-141316600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:141289200-141309000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:141289200-141316400	Strong transcription	Fetal Thymus	thymus
50	chr3:141289400-141295000	Strong transcription	Placenta	Placenta

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