Variant report

Variant	rs9849180
Chromosome Location	chr3:141254835-141254836
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	chr3:141247002..141250930-chr3:141252539..141256431,5	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1077181	0.92[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs11557453	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs11707656	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11708253	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709875	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711318	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11713714	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11714208	0.88[CEU][hapmap];0.93[MEX][hapmap]
rs11716776	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717144	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs11717842	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695734	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695735	0.91[CEU][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695736	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695740	0.92[CEU][hapmap];0.92[MEX][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12695741	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12695743	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs13059128	0.84[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes]
rs13068454	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13072100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083593	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088429	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095168	0.96[CEU][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13098300	0.82[AMR][1000 genomes]
rs13099945	0.96[CEU][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1863870	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312194	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2312266	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34317570	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34342794	0.95[EUR][1000 genomes]
rs3806647	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4334619	0.83[EUR][1000 genomes]
rs71619392	0.92[EUR][1000 genomes]
rs720663	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7636914	0.96[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs7651511	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9289629	0.92[CEU][hapmap];0.93[MEX][hapmap]
rs9289634	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9808953	0.96[CEU][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9822575	0.96[CEU][hapmap];0.93[MEX][hapmap];0.83[EUR][1000 genomes]
rs9823528	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9829588	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9830055	0.96[CEU][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9833121	0.96[CEU][hapmap];0.93[MEX][hapmap];0.83[EUR][1000 genomes]
rs9836050	0.96[CEU][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9836818	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9837202	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838230	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9838419	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9840159	0.83[EUR][1000 genomes]
rs9840697	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9843866	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9850416	0.96[CEU][hapmap];0.93[MEX][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9865971	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9868956	0.96[CEU][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9870749	0.96[CEU][hapmap];0.93[MEX][hapmap];0.83[EUR][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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9849180	RASA2	cis	cerebellum	SCAN
rs9849180	ATR	cis	parietal	SCAN
rs9849180	RASA2	cis	parietal	SCAN
rs9849180	ZBTB38	cis	cerebellum	SCAN
rs9849180	GK5	cis	parietal	SCAN
rs9849180	ATP1B3	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141207000-141255000	Weak transcription	Aorta	Aorta
2	chr3:141217800-141258400	Weak transcription	Psoas Muscle	Psoas
3	chr3:141229400-141267400	Weak transcription	Fetal Heart	heart
4	chr3:141230000-141259800	Weak transcription	Small Intestine	intestine
5	chr3:141231600-141263600	Weak transcription	Fetal Brain Male	brain
6	chr3:141236200-141281600	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:141236400-141276000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:141236400-141301000	Weak transcription	Brain Substantia Nigra	brain
9	chr3:141236400-141306600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:141236600-141263200	Weak transcription	Brain Germinal Matrix	brain
11	chr3:141236600-141275800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:141236600-141297000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:141236600-141299400	Weak transcription	Gastric	stomach
14	chr3:141237000-141265400	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:141237000-141299400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:141241800-141263600	Weak transcription	Fetal Brain Female	brain
17	chr3:141242200-141263600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:141242200-141274800	Weak transcription	Lung	lung
19	chr3:141243400-141299400	Weak transcription	Spleen	Spleen
20	chr3:141243600-141263600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:141246000-141278400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:141249200-141257200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:141249200-141258200	Weak transcription	Brain Anterior Caudate	brain
24	chr3:141249200-141274600	Weak transcription	Liver	Liver
25	chr3:141249800-141260600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:141249800-141260600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:141250600-141257000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr3:141250800-141255600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:141250800-141261000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr3:141251200-141257800	Weak transcription	HMEC	breast
31	chr3:141251400-141257000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr3:141251400-141257400	Weak transcription	Hela-S3	cervix
33	chr3:141251800-141255200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:141252200-141256400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:141252200-141262200	Weak transcription	HSMMtube	muscle
36	chr3:141252800-141256800	Strong transcription	HSMM	muscle
37	chr3:141253000-141256400	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:141253000-141257400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:141253200-141255200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:141253800-141255000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:141253800-141255000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr3:141253800-141255400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:141253800-141255400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:141253800-141255400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:141253800-141255400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:141253800-141255600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:141253800-141256800	Strong transcription	Primary T cells from cord blood	blood
48	chr3:141254000-141255400	Strong transcription	Osteobl	bone
49	chr3:141254000-141255600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:141254000-141256000	Strong transcription	Primary T helper cells PMA-I stimulated	--

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