Variant report

Variant	rs11713693
Chromosome Location	chr3:47074906-47074907
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47072469..47075207-chr3:47077387..47079210,2	K562	blood:
2	chr3:47074366..47076191-chr3:47079494..47081958,2	K562	blood:
3	chr3:47069157..47071799-chr3:47073550..47075911,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10433549	0.87[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10461018	0.91[YRI][hapmap]
rs11130115	0.81[CEU][hapmap]
rs11707736	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11709660	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11714373	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11715121	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719738	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11720139	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11917361	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11923706	0.91[ASN][1000 genomes]
rs12493425	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12631730	0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs12715421	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13061071	0.81[CEU][hapmap]
rs1466740	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1466741	0.80[CEU][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs17784127	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1811652	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2061197	0.91[YRI][hapmap]
rs2132173	0.81[CEU][hapmap]
rs2278963	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305634	0.81[CEU][hapmap]
rs2305635	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34103310	0.81[EUR][1000 genomes]
rs4018905	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4078466	0.85[CEU][hapmap]
rs4082155	0.85[CEU][hapmap]
rs4682844	0.91[YRI][hapmap]
rs4683296	0.82[YRI][hapmap]
rs4683297	0.91[YRI][hapmap]
rs4683322	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55724164	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55927279	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56217494	0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56249396	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57756484	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs58956475	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs62246398	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62246402	0.81[AFR][1000 genomes]
rs62246451	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs62246455	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6414435	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6414436	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442055	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442059	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6442060	0.81[ASN][1000 genomes]
rs6766230	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6767218	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6767907	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6768722	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6773521	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6777145	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781941	0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6791062	0.94[ASN][1000 genomes]
rs7373821	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7433300	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs749511	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs749512	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7610620	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7620997	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7621911	0.85[AFR][1000 genomes]
rs7623888	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7633435	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7645278	0.91[YRI][hapmap]
rs9311403	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9812878	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9818382	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9821119	0.91[ASN][1000 genomes]
rs9837343	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9844122	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9845728	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9854790	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9858443	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9875235	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	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
5	nsv997261	chr3:47054766-47133680	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11713693	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs11713693	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs11713693	DHX30	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47061000-47076200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:47061000-47079000	Weak transcription	Fetal Brain Male	brain
3	chr3:47061200-47076000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:47061200-47083000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:47061400-47076000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:47061400-47076200	Weak transcription	HSMMtube	muscle
7	chr3:47062000-47075400	Weak transcription	A549	lung
8	chr3:47062200-47075000	Weak transcription	Brain Germinal Matrix	brain
9	chr3:47062200-47075400	Weak transcription	Aorta	Aorta
10	chr3:47062200-47076000	Weak transcription	Fetal Kidney	kidney
11	chr3:47062200-47077800	Weak transcription	Colonic Mucosa	Colon
12	chr3:47062800-47075400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:47062800-47076400	Weak transcription	Fetal Brain Female	brain
14	chr3:47063200-47079000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:47064400-47076600	Weak transcription	Psoas Muscle	Psoas
16	chr3:47064400-47079000	Weak transcription	Pancreas	Pancrea
17	chr3:47064400-47079000	Weak transcription	Right Ventricle	heart
18	chr3:47064600-47075400	Weak transcription	NHLF	lung
19	chr3:47064600-47076400	Weak transcription	Small Intestine	intestine
20	chr3:47064800-47076600	Weak transcription	Gastric	stomach
21	chr3:47065000-47077000	Weak transcription	Stomach Mucosa	stomach
22	chr3:47066800-47075600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:47066800-47075800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:47066800-47076000	Weak transcription	Brain Anterior Caudate	brain
25	chr3:47066800-47076000	Weak transcription	NHDF-Ad	bronchial
26	chr3:47066800-47076600	Weak transcription	Esophagus	oesophagus
27	chr3:47066800-47079000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:47067000-47075600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:47067000-47075800	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:47067000-47076200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:47067000-47076600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:47067200-47076000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:47067200-47076000	Weak transcription	Brain Substantia Nigra	brain
34	chr3:47067200-47076000	Weak transcription	K562	blood
35	chr3:47067400-47076000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:47069000-47079000	Strong transcription	Dnd41	blood
37	chr3:47069400-47079000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr3:47069400-47079000	Strong transcription	Fetal Thymus	thymus
39	chr3:47069600-47079000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:47069600-47088200	Strong transcription	Liver	Liver
41	chr3:47069600-47088200	Strong transcription	Fetal Intestine Large	intestine
42	chr3:47069600-47089000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:47069800-47079000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:47069800-47086600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:47070200-47075400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr3:47070200-47080600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:47070400-47076000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:47070400-47079000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr3:47070400-47079000	Weak transcription	Fetal Heart	heart
50	chr3:47070400-47089000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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