Variant report

Variant	rs17784127
Chromosome Location	chr3:47061700-47061701
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47056274..47058537-chr3:47060198..47062486,2	K562	blood:
2	chr3:47051592..47055905-chr3:47059567..47061970,4	K562	blood:

Variant related genes	Relation type
ENSG00000236409	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10433549	0.96[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10461018	0.85[CEU][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs1079276	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1108301	0.85[EUR][1000 genomes]
rs11130110	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs11130111	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs11130112	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs11130115	0.88[CEU][hapmap]
rs11707736	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11709660	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11713693	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11714373	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11715121	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719738	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11720139	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11917361	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11917474	0.84[EUR][1000 genomes]
rs11923706	0.89[ASN][1000 genomes]
rs12152493	0.83[EUR][1000 genomes]
rs12491473	0.82[EUR][1000 genomes]
rs12493425	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12630534	0.82[EUR][1000 genomes]
rs12631730	0.90[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs12715421	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13061071	0.88[CEU][hapmap]
rs13062681	0.89[EUR][1000 genomes]
rs13066214	0.87[EUR][1000 genomes]
rs13077398	0.84[EUR][1000 genomes]
rs13091054	0.81[EUR][1000 genomes]
rs1463393	0.82[EUR][1000 genomes]
rs1466740	0.82[ASN][1000 genomes]
rs1466741	0.92[CEU][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs1811652	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1869869	0.84[EUR][1000 genomes]
rs2061197	0.85[CEU][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs2132173	0.88[CEU][hapmap]
rs2278963	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305634	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs2305635	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305638	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2385867	0.91[EUR][1000 genomes]
rs34103310	0.85[EUR][1000 genomes]
rs34344887	0.86[EUR][1000 genomes]
rs4018905	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4078466	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4082155	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4234465	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs4682831	0.85[EUR][1000 genomes]
rs4682837	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs4682844	0.85[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs4682852	0.89[CEU][hapmap]
rs4683296	0.82[YRI][hapmap]
rs4683297	0.91[YRI][hapmap]
rs4683322	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55724164	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55843455	0.85[EUR][1000 genomes]
rs55927279	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56217494	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56249396	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57756484	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs58956475	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs61729713	0.85[EUR][1000 genomes]
rs62246375	0.85[EUR][1000 genomes]
rs62246398	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62246451	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62246455	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62248439	0.82[EUR][1000 genomes]
rs6414435	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6414436	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6442055	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6442059	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442060	0.81[ASN][1000 genomes]
rs66539935	0.85[EUR][1000 genomes]
rs66564457	0.82[EUR][1000 genomes]
rs6763236	0.84[EUR][1000 genomes]
rs6766230	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6767218	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6767907	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6768722	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6772670	0.91[CEU][hapmap]
rs6773521	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6774733	0.81[EUR][1000 genomes]
rs6777145	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6781941	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6791062	0.91[ASN][1000 genomes]
rs6794193	0.82[EUR][1000 genomes]
rs6808742	0.84[EUR][1000 genomes]
rs7373821	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7426969	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7433300	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs749511	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs749512	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7610620	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7610636	0.90[EUR][1000 genomes]
rs7617689	0.82[EUR][1000 genomes]
rs7620997	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7621911	0.82[AFR][1000 genomes]
rs7623888	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7625067	0.83[EUR][1000 genomes]
rs7625070	0.83[EUR][1000 genomes]
rs7628747	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7633435	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7633698	0.84[EUR][1000 genomes]
rs7636252	0.84[EUR][1000 genomes]
rs7637302	0.82[EUR][1000 genomes]
rs7640397	0.81[EUR][1000 genomes]
rs7645278	0.91[YRI][hapmap]
rs9311403	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9812878	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9818382	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9821119	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9837343	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9844122	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9845728	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9854790	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9858443	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9875235	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[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
rs17784127	DHX30	cis	multi-tissue	Pritchard
rs17784127	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs17784127	SETD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47050200-47063800	Weak transcription	Stomach Mucosa	stomach
2	chr3:47051400-47064000	Weak transcription	Small Intestine	intestine
3	chr3:47051800-47062000	Weak transcription	Psoas Muscle	Psoas
4	chr3:47052000-47062200	Strong transcription	Fetal Stomach	stomach
5	chr3:47053200-47062400	Strong transcription	Fetal Muscle Trunk	muscle
6	chr3:47053400-47062200	Strong transcription	Fetal Muscle Leg	muscle
7	chr3:47054000-47061800	Strong transcription	Placenta	Placenta
8	chr3:47054200-47062400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:47054400-47062000	Strong transcription	Adipose Nuclei	Adipose
10	chr3:47054600-47062800	Strong transcription	Fetal Brain Female	brain
11	chr3:47055000-47062000	Strong transcription	Brain Cingulate Gyrus	brain
12	chr3:47055000-47062400	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:47055400-47061800	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr3:47055400-47062200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:47055400-47063000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:47055600-47061800	Strong transcription	Brain Angular Gyrus	brain
17	chr3:47055600-47062000	Strong transcription	Brain Substantia Nigra	brain
18	chr3:47055600-47062000	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr3:47056400-47061800	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:47056600-47062200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:47056800-47061800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:47056800-47062000	Strong transcription	Fetal Lung	lung
23	chr3:47056800-47062400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:47057200-47066600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:47057800-47062200	Strong transcription	Aorta	Aorta
26	chr3:47057800-47062200	Strong transcription	Fetal Kidney	kidney
27	chr3:47058000-47062000	Strong transcription	Brain Anterior Caudate	brain
28	chr3:47058000-47062000	Genic enhancers	HepG2	liver
29	chr3:47058000-47062400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:47058200-47062200	Strong transcription	Brain Germinal Matrix	brain
31	chr3:47058200-47062200	Strong transcription	Colonic Mucosa	Colon
32	chr3:47058200-47062200	Genic enhancers	GM12878-XiMat	blood
33	chr3:47058200-47063000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
34	chr3:47058400-47061800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:47058600-47062200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr3:47058800-47069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:47059000-47062000	Strong transcription	A549	lung
38	chr3:47059200-47062000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:47059200-47062000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:47059400-47062000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr3:47059400-47062200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr3:47059400-47062200	Strong transcription	NHLF	lung
43	chr3:47059400-47066400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:47059400-47066400	Strong transcription	Primary T cells from cord blood	blood
45	chr3:47059600-47061800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr3:47059600-47061800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:47059600-47062000	Strong transcription	Liver	Liver
48	chr3:47059800-47061800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:47059800-47061800	Strong transcription	Osteobl	bone
50	chr3:47059800-47062200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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