Variant report

Variant	rs11710121
Chromosome Location	chr3:47351501-47351502
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1038394	0.88[CEU][hapmap]
rs10490798	0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs1076394	0.92[ASW][hapmap];0.85[CEU][hapmap];0.84[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10865946	0.88[CEU][hapmap]
rs11130123	0.82[CEU][hapmap]
rs11130124	0.85[CEU][hapmap]
rs11130126	0.92[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11130128	0.88[CEU][hapmap]
rs11130129	0.88[CEU][hapmap]
rs11705957	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs11710013	0.85[CEU][hapmap]
rs11710322	0.92[ASW][hapmap];0.85[CEU][hapmap];0.84[LWK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11711824	0.88[CEU][hapmap]
rs11712445	0.91[CEU][hapmap]
rs11716763	0.88[CEU][hapmap]
rs11719877	0.88[CEU][hapmap]
rs11720439	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11915074	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11920853	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11921117	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12636851	0.88[CEU][hapmap]
rs13059519	0.88[CEU][hapmap]
rs13072802	0.80[EUR][1000 genomes]
rs13075233	0.88[CEU][hapmap]
rs13094438	0.85[CEU][hapmap]
rs1466741	0.83[YRI][hapmap]
rs1531875	0.88[CEU][hapmap]
rs1638676	0.85[CEU][hapmap]
rs17410853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs17411375	0.85[CEU][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap]
rs17476234	0.82[AFR][1000 genomes]
rs17784882	0.88[CEU][hapmap]
rs1872164	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs2101247	0.85[CEU][hapmap]
rs2159400	0.85[CEU][hapmap]
rs2240796	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2276853	0.85[CEU][hapmap]
rs2276854	0.85[CEU][hapmap]
rs295428	0.85[CEU][hapmap]
rs295441	0.85[CEU][hapmap]
rs295442	0.85[CEU][hapmap]
rs295449	0.85[CEU][hapmap]
rs295458	0.85[CEU][hapmap]
rs295461	0.85[CEU][hapmap]
rs3736177	0.87[CEU][hapmap]
rs3816779	0.88[CEU][hapmap]
rs4683326	0.87[CEU][hapmap]
rs4858811	0.88[CEU][hapmap]
rs4858824	0.88[CEU][hapmap]
rs4858868	0.88[CEU][hapmap]
rs4858893	0.88[CEU][hapmap]
rs4858894	0.82[CEU][hapmap]
rs59689369	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6767907	0.92[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.86[YRI][hapmap]
rs6768221	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6772670	0.83[CEU][hapmap]
rs6780013	0.96[CEU][hapmap];0.90[GIH][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap]
rs6791842	0.85[CEU][hapmap]
rs6792461	0.88[CEU][hapmap]
rs6800271	0.88[CEU][hapmap]
rs73069104	0.81[AMR][1000 genomes]
rs7651762	0.88[CEU][hapmap]
rs807932	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs807936	0.85[CEU][hapmap]
rs811115	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs878659	0.88[CEU][hapmap]
rs922957	0.88[CEU][hapmap]
rs9683033	0.88[CEU][hapmap]
rs9837343	0.92[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.86[YRI][hapmap]

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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11710121	LRRC2	cis	cerebellum	SCAN
rs11710121	HYAL2	cis	cerebellum	SCAN
rs11710121	QRICH1	cis	parietal	SCAN
rs11710121	SCAP	cis	parietal	SCAN
rs11710121	PRKAR2A	cis	cerebellum	SCAN
rs11710121	C3orf75	cis	cerebellum	SCAN
rs11710121	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs11710121	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs11710121	IFRD2	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47325400-47361000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:47325600-47367600	Weak transcription	A549	lung
3	chr3:47325800-47352000	Weak transcription	Fetal Kidney	kidney
4	chr3:47326200-47356200	Weak transcription	Fetal Heart	heart
5	chr3:47326200-47356600	Weak transcription	NHDF-Ad	bronchial
6	chr3:47326200-47359600	Weak transcription	Fetal Lung	lung
7	chr3:47326200-47362200	Weak transcription	Gastric	stomach
8	chr3:47326200-47363200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:47326400-47364400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:47326600-47351600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:47326800-47356600	Weak transcription	Small Intestine	intestine
12	chr3:47328400-47364400	Weak transcription	Pancreas	Pancrea
13	chr3:47329200-47359800	Weak transcription	NHLF	lung
14	chr3:47330400-47352000	Weak transcription	NHEK	skin
15	chr3:47330400-47356000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:47330600-47359800	Weak transcription	Hela-S3	cervix
17	chr3:47330600-47360600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:47330800-47356600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:47330800-47361800	Weak transcription	HMEC	breast
20	chr3:47332200-47361800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:47332400-47355600	Weak transcription	Brain Substantia Nigra	brain
22	chr3:47332600-47361000	Weak transcription	Esophagus	oesophagus
23	chr3:47332800-47361000	Weak transcription	Aorta	Aorta
24	chr3:47333000-47356400	Weak transcription	Osteobl	bone
25	chr3:47333200-47364800	Weak transcription	NH-A	brain
26	chr3:47333800-47371400	Weak transcription	Psoas Muscle	Psoas
27	chr3:47336400-47360200	Weak transcription	Thymus	Thymus
28	chr3:47337000-47356600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:47337000-47361000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:47338400-47361200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:47338600-47355600	Weak transcription	Left Ventricle	heart
32	chr3:47338600-47361200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:47338600-47369800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:47338600-47371200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:47338800-47351600	Weak transcription	Fetal Thymus	thymus
36	chr3:47338800-47356200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:47338800-47360200	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:47339000-47356200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:47339000-47359400	Weak transcription	Spleen	Spleen
40	chr3:47339000-47361800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr3:47341600-47360000	Weak transcription	Fetal Intestine Large	intestine
42	chr3:47343200-47362000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:47343800-47354800	Weak transcription	HepG2	liver
44	chr3:47344200-47355200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:47344200-47356400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:47344400-47351600	Weak transcription	Lung	lung
47	chr3:47344400-47356200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:47344400-47356200	Weak transcription	HUVEC	blood vessel
49	chr3:47344400-47362200	Weak transcription	Brain Germinal Matrix	brain
50	chr3:47344600-47356600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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