Variant report

Variant	rs720663
Chromosome Location	chr3:141233105-141233106
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141232140..141234840-chr3:141247609..141249349,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1077181	0.88[CEU][hapmap];0.93[MEX][hapmap]
rs11557453	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11707656	0.85[EUR][1000 genomes]
rs11708253	0.83[EUR][1000 genomes]
rs11709875	0.92[CEU][hapmap];0.93[MEX][hapmap]
rs11711318	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11713714	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11714208	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11716776	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11717144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11717842	0.96[CEU][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12695734	0.83[EUR][1000 genomes]
rs12695735	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs12695736	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12695740	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12695741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12695743	0.86[ASW][hapmap];0.92[CEU][hapmap];0.81[GIH][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13059128	0.80[CEU][hapmap];0.93[MEX][hapmap]
rs13062809	0.87[ASN][1000 genomes]
rs13067519	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13068454	0.80[EUR][1000 genomes]
rs13072100	0.96[CEU][hapmap];0.85[MEX][hapmap];0.85[EUR][1000 genomes]
rs13078872	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13083593	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13084444	0.96[CEU][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13088429	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs13095168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863870	0.92[CEU][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs2312194	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34317570	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34342794	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732872	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3806647	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4334619	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6769161	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs71619392	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7624941	1.00[JPT][hapmap]
rs7636914	0.85[MEX][hapmap]
rs7649666	1.00[JPT][hapmap]
rs7651511	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9289629	0.96[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9289634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9808953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9822575	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9823528	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9829588	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9830055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9833121	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9836050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837202	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs9838230	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838419	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9840159	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9840697	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843866	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9849180	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9850416	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9851256	1.00[CHB][hapmap]
rs9865971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9870749	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9873042	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs720663	RASA2	cis	cerebellum	SCAN
rs720663	ATP1B3	cis	cerebellum	SCAN
rs720663	GK5	cis	parietal	SCAN
rs720663	ZBTB38	cis	cerebellum	SCAN
rs720663	ACPL2	cis	lymphoblastoid	seeQTL
rs720663	RASA2	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141207000-141235800	Weak transcription	Gastric	stomach
2	chr3:141207000-141255000	Weak transcription	Aorta	Aorta
3	chr3:141207800-141233200	Weak transcription	Fetal Intestine Large	intestine
4	chr3:141207800-141235600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr3:141209800-141234200	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:141210400-141248000	Weak transcription	NHLF	lung
7	chr3:141211400-141235400	Weak transcription	A549	lung
8	chr3:141216000-141239600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:141217800-141235800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr3:141217800-141258400	Weak transcription	Psoas Muscle	Psoas
11	chr3:141218000-141235400	Weak transcription	NHEK	skin
12	chr3:141218200-141235600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:141218400-141233200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr3:141218400-141233400	Weak transcription	HMEC	breast
15	chr3:141218600-141235400	Weak transcription	Brain Germinal Matrix	brain
16	chr3:141218800-141235600	Weak transcription	Left Ventricle	heart
17	chr3:141219000-141233200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:141219000-141235200	Weak transcription	Hela-S3	cervix
19	chr3:141219000-141235400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:141219000-141235600	Weak transcription	Fetal Intestine Small	intestine
21	chr3:141219200-141235200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:141221000-141235600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:141221200-141235400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:141221400-141235000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:141221600-141235600	Weak transcription	Fetal Stomach	stomach
26	chr3:141221800-141235400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:141222400-141233200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:141224600-141233400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:141225600-141233200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:141226200-141235600	Weak transcription	Thymus	Thymus
31	chr3:141226400-141235200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:141226400-141235400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:141226600-141235600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:141226600-141235600	Weak transcription	Pancreas	Pancrea
35	chr3:141226600-141235600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:141226600-141235800	Weak transcription	Brain Angular Gyrus	brain
37	chr3:141226600-141236200	Weak transcription	Brain Substantia Nigra	brain
38	chr3:141226600-141254400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:141226800-141233200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:141226800-141235400	Weak transcription	HepG2	liver
41	chr3:141227400-141242800	Weak transcription	Ovary	ovary
42	chr3:141227600-141235800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:141227600-141236200	Weak transcription	Lung	lung
44	chr3:141228400-141246600	Strong transcription	Dnd41	blood
45	chr3:141229000-141234400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
46	chr3:141229000-141236200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:141229200-141235400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:141229200-141236200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr3:141229400-141235600	Strong transcription	Primary B cells from cord blood	blood
50	chr3:141229400-141267400	Weak transcription	Fetal Heart	heart

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