Variant report

Variant	rs11915074
Chromosome Location	chr3:47309757-47309758
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47308251..47310549-chr3:47311430..47313060,2	K562	blood:
2	chr3:47308967..47310728-chr3:47443375..47445366,2	K562	blood:
3	chr3:47308470..47309990-chr3:47311711..47314511,2	K562	blood:
4	chr3:47308250..47310390-chr3:47316746..47318769,2	MCF-7	breast:
5	chr3:47308440..47310192-chr3:47315803..47317741,2	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1038394	0.88[CEU][hapmap]
rs10490798	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1076394	0.92[CEU][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs10865946	0.89[CEU][hapmap]
rs11130115	0.82[CEU][hapmap]
rs11130123	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs11130124	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11130126	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];0.99[ASN][1000 genomes]
rs11130128	0.89[CEU][hapmap]
rs11130129	0.88[CEU][hapmap]
rs11705957	0.88[CEU][hapmap]
rs11710013	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs11710121	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]
rs11710322	0.92[CEU][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs11711824	0.88[CEU][hapmap]
rs11712445	0.92[CEU][hapmap]
rs11714294	0.85[EUR][1000 genomes]
rs11719877	0.88[CEU][hapmap]
rs11720439	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11920354	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11920853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11921117	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11925560	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12631730	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs12636851	0.88[CEU][hapmap]
rs13061071	0.82[CEU][hapmap]
rs13075233	0.88[CEU][hapmap]
rs13094438	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs1466740	0.90[AFR][1000 genomes]
rs1466741	0.84[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1531875	0.88[CEU][hapmap]
rs1638676	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs17410853	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17411375	0.92[CEU][hapmap]
rs17476234	0.87[EUR][1000 genomes]
rs1872164	0.88[CEU][hapmap]
rs2088135	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2101247	0.84[CEU][hapmap]
rs2132173	0.81[CEU][hapmap]
rs2159400	0.92[CEU][hapmap]
rs2240796	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2276853	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2276854	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs295428	0.92[CEU][hapmap]
rs295441	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs295442	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs295449	0.92[CEU][hapmap]
rs295458	0.92[CEU][hapmap]
rs295461	0.92[CEU][hapmap]
rs3736177	0.88[CEU][hapmap]
rs4682852	0.83[CEU][hapmap]
rs4683326	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs4858811	0.89[CEU][hapmap]
rs4858824	0.89[CEU][hapmap]
rs4858868	0.88[CEU][hapmap]
rs4858893	0.89[CEU][hapmap]
rs4858894	0.84[CEU][hapmap]
rs56250009	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57756484	0.83[AFR][1000 genomes]
rs58472056	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61386020	0.84[ASN][1000 genomes]
rs62246455	0.83[AFR][1000 genomes]
rs62248905	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6767907	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs6768221	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6772670	0.92[CEU][hapmap]
rs6773521	0.83[AFR][1000 genomes]
rs6780013	0.96[CEU][hapmap]
rs6781941	0.83[AFR][1000 genomes]
rs6791842	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs6792461	0.88[CEU][hapmap]
rs6800271	0.88[CEU][hapmap]
rs73069104	0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7433300	0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs7632501	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7636423	0.90[EUR][1000 genomes]
rs7651762	0.88[CEU][hapmap]
rs807932	0.88[CEU][hapmap]
rs807935	0.85[EUR][1000 genomes]
rs807936	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs807937	0.86[EUR][1000 genomes]
rs811115	0.87[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs878659	0.88[CEU][hapmap]
rs922957	0.89[CEU][hapmap]
rs9311403	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap]
rs9683033	0.88[CEU][hapmap]
rs9837343	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs9845728	0.81[AFR][1000 genomes]
rs9854790	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11915074	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs11915074	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs11915074	DHX30	cis	multi-tissue	Pritchard

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47264200-47322200	Weak transcription	Gastric	stomach
2	chr3:47282800-47322400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:47285400-47315800	Weak transcription	Pancreas	Pancrea
4	chr3:47285600-47312400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:47293600-47323200	Weak transcription	Spleen	Spleen
6	chr3:47300800-47322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:47301000-47322800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:47301200-47323000	Weak transcription	Psoas Muscle	Psoas
9	chr3:47302600-47314600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:47302600-47322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:47302800-47323200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:47305600-47323200	Weak transcription	Primary T cells from cord blood	blood
13	chr3:47305800-47315000	Weak transcription	Fetal Intestine Small	intestine
14	chr3:47306800-47310000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr3:47307000-47314800	Weak transcription	Lung	lung
16	chr3:47307200-47309800	Enhancers	Dnd41	blood
17	chr3:47307200-47310800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:47307800-47311000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:47308200-47314400	Weak transcription	Right Ventricle	heart
20	chr3:47308400-47314800	Weak transcription	Fetal Stomach	stomach
21	chr3:47308600-47315400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:47308600-47322200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:47308600-47322400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:47308600-47323000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:47308600-47323200	Weak transcription	Esophagus	oesophagus
26	chr3:47308800-47310400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:47308800-47311800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr3:47308800-47314600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:47308800-47316400	Weak transcription	Left Ventricle	heart
30	chr3:47308800-47318000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:47308800-47322200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:47308800-47322200	Weak transcription	Hela-S3	cervix
33	chr3:47308800-47322200	Weak transcription	HepG2	liver
34	chr3:47308800-47322200	Weak transcription	NHEK	skin
35	chr3:47308800-47322400	Weak transcription	A549	lung
36	chr3:47308800-47322600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:47308800-47322600	Weak transcription	Brain Anterior Caudate	brain
38	chr3:47308800-47322600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:47308800-47322800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:47308800-47322800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:47308800-47323000	Weak transcription	Adipose Nuclei	Adipose
42	chr3:47308800-47323000	Weak transcription	Brain Substantia Nigra	brain
43	chr3:47309000-47310600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr3:47309000-47314800	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:47309000-47316000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:47309000-47322200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:47309000-47322200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:47309000-47322400	Weak transcription	Placenta	Placenta
49	chr3:47309000-47322600	Weak transcription	HUVEC	blood vessel
50	chr3:47309000-47322800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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