Variant report

Variant	rs1493209
Chromosome Location	chr3:141292618-141292619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141287617..141290241-chr3:141292513..141294840,2	K562	blood:
2	chr3:141279547..141282126-chr3:141289816..141292776,2	K562	blood:
3	chr3:141291433..141293078-chr3:141457049..141459142,2	MCF-7	breast:
4	chr3:141292412..141295097-chr3:141295843..141298423,3	K562	blood:
5	chr3:141173922..141177182-chr3:141288723..141292910,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114125	Chromatin interaction
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11711375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11916906	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11917587	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13062809	0.90[EUR][1000 genomes]
rs13069717	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1366042	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1582875	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs16851435	0.89[JPT][hapmap]
rs16851438	0.94[JPT][hapmap]
rs16851441	0.89[JPT][hapmap]
rs16851483	0.88[JPT][hapmap]
rs1863867	0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2035935	0.88[JPT][hapmap]
rs2035936	0.82[JPT][hapmap]
rs2042864	0.96[CEU][hapmap]
rs2172471	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2312193	0.92[CEU][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs2639997	0.88[JPT][hapmap]
rs2639998	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2640017	0.88[JPT][hapmap]
rs295299	0.88[JPT][hapmap]
rs295300	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs295320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs295323	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35711802	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732869	0.89[JPT][hapmap]
rs3806646	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3821709	0.88[JPT][hapmap]
rs3821710	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821712	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683610	0.88[JPT][hapmap]
rs6440013	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440015	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6763498	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6767158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6776003	0.86[CEU][hapmap];0.91[ASN][1000 genomes]
rs6785874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6795168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6800122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6808837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7627807	0.88[JPT][hapmap]
rs7632308	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7643837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9813177	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9851256	0.88[CEU][hapmap]
rs9878347	0.94[JPT][hapmap]
rs9879503	0.94[JPT][hapmap]

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
rs1493209	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	chr3:141254600-141294400	Weak transcription	Esophagus	oesophagus
8	chr3:141254800-141295200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:141254800-141299200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:141254800-141299400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:141254800-141299400	Weak transcription	Right Ventricle	heart
12	chr3:141254800-141319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:141255200-141304800	Weak transcription	Ovary	ovary
14	chr3:141255200-141320000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:141255400-141319200	Weak transcription	Aorta	Aorta
16	chr3:141257000-141300200	Weak transcription	Pancreas	Pancrea
17	chr3:141265200-141336200	Weak transcription	Psoas Muscle	Psoas
18	chr3:141267400-141295000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:141268400-141297800	Weak transcription	Fetal Heart	heart
20	chr3:141269200-141294400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:141271200-141299400	Weak transcription	Brain Angular Gyrus	brain
22	chr3:141272600-141319200	Strong transcription	Dnd41	blood
23	chr3:141275800-141320600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:141276000-141299400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:141276200-141297000	Weak transcription	Lung	lung
26	chr3:141276400-141329400	Weak transcription	Small Intestine	intestine
27	chr3:141277200-141297000	Weak transcription	Thymus	Thymus
28	chr3:141277200-141341400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr3:141277400-141293600	Weak transcription	Fetal Kidney	kidney
30	chr3:141277600-141296400	Weak transcription	Hela-S3	cervix
31	chr3:141277800-141312000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr3:141278000-141296800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:141281800-141297000	Weak transcription	Fetal Intestine Small	intestine
34	chr3:141281800-141329400	Weak transcription	Fetal Brain Male	brain
35	chr3:141283400-141295000	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:141284600-141299200	Weak transcription	Fetal Stomach	stomach
37	chr3:141288000-141312400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:141288200-141294400	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:141288200-141294800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:141288200-141295200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:141288200-141320000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:141288400-141294200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:141288400-141294400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:141288400-141295200	Strong transcription	Primary B cells from cord blood	blood
45	chr3:141288400-141316400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr3:141288600-141292800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:141288600-141292800	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr3:141288600-141293000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:141288600-141294600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:141288600-141295000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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