Variant report

Variant	rs12631730
Chromosome Location	chr3:47129903-47129904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1024036	0.82[LWK][hapmap];0.85[YRI][hapmap]
rs10433549	0.84[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs10461017	0.95[YRI][hapmap]
rs10461019	0.95[YRI][hapmap]
rs10490798	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs11130108	0.85[YRI][hapmap]
rs11130126	0.90[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap]
rs11707736	0.84[ASN][1000 genomes]
rs11708257	0.95[YRI][hapmap]
rs11709660	0.83[ASN][1000 genomes]
rs11709876	0.86[YRI][hapmap]
rs11713537	0.95[YRI][hapmap]
rs11713693	0.84[ASN][1000 genomes]
rs11715121	0.85[ASN][1000 genomes]
rs11719738	0.83[ASN][1000 genomes]
rs11720139	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs11915074	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs11917361	0.85[ASN][1000 genomes]
rs11920853	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs11923706	0.82[ASN][1000 genomes]
rs11928558	0.95[YRI][hapmap]
rs12493425	0.84[ASN][1000 genomes]
rs12715421	0.86[ASN][1000 genomes]
rs13323092	1.00[YRI][hapmap]
rs1378818	0.95[YRI][hapmap]
rs1463394	0.86[YRI][hapmap]
rs17784127	0.90[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1869870	0.94[YRI][hapmap]
rs2124509	0.95[YRI][hapmap]
rs2278963	0.90[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2305635	0.84[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs2385868	0.86[YRI][hapmap]
rs2385869	0.95[YRI][hapmap]
rs2891893	0.86[YRI][hapmap]
rs4018904	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs4018905	0.85[ASN][1000 genomes]
rs4282092	0.82[LWK][hapmap];0.95[YRI][hapmap]
rs4289375	0.81[YRI][hapmap]
rs4373094	0.95[YRI][hapmap]
rs4478107	0.90[YRI][hapmap]
rs4543047	0.86[YRI][hapmap]
rs4682832	0.82[YRI][hapmap]
rs4682838	0.82[YRI][hapmap]
rs4683282	0.86[YRI][hapmap]
rs4683283	0.85[YRI][hapmap]
rs4683284	0.95[YRI][hapmap]
rs4683285	0.86[YRI][hapmap]
rs4683286	0.85[YRI][hapmap]
rs4683290	0.85[YRI][hapmap]
rs4683291	0.90[YRI][hapmap]
rs4683322	0.90[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs55927279	0.83[ASN][1000 genomes]
rs56217494	0.81[ASN][1000 genomes]
rs56249396	0.82[ASN][1000 genomes]
rs59299766	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60965459	0.86[ASN][1000 genomes]
rs62246398	0.83[ASN][1000 genomes]
rs6414435	0.87[ASN][1000 genomes]
rs6414436	0.87[ASN][1000 genomes]
rs6442043	0.82[YRI][hapmap]
rs6442044	0.86[YRI][hapmap]
rs6442047	0.86[YRI][hapmap]
rs6442055	0.87[ASN][1000 genomes]
rs6442059	0.84[ASN][1000 genomes]
rs6442060	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6766230	0.82[ASN][1000 genomes]
rs6766676	0.86[YRI][hapmap]
rs6767218	0.83[ASN][1000 genomes]
rs6767907	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs6768722	0.86[ASN][1000 genomes]
rs6772449	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs6777145	0.87[ASN][1000 genomes]
rs6778673	0.82[LWK][hapmap];0.90[YRI][hapmap]
rs6778687	0.95[YRI][hapmap]
rs6787210	0.95[YRI][hapmap]
rs6791062	0.84[ASN][1000 genomes]
rs6806521	0.85[YRI][hapmap]
rs6809904	0.82[YRI][hapmap]
rs7433300	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs749511	0.85[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap]
rs749512	0.85[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap]
rs7610620	0.84[ASN][1000 genomes]
rs7623888	0.82[ASN][1000 genomes]
rs7624549	0.86[YRI][hapmap]
rs7625011	0.85[YRI][hapmap]
rs7630154	1.00[YRI][hapmap]
rs7630904	0.82[YRI][hapmap]
rs7633435	0.84[ASN][1000 genomes]
rs7638549	0.95[YRI][hapmap]
rs7639121	0.88[LWK][hapmap];0.95[YRI][hapmap]
rs7643868	0.82[YRI][hapmap]
rs7644382	1.00[YRI][hapmap]
rs7646076	0.86[YRI][hapmap]
rs7649413	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs7649941	0.89[YRI][hapmap]
rs7650142	0.81[YRI][hapmap]
rs903538	0.82[LWK][hapmap];0.90[YRI][hapmap]
rs924009	0.80[YRI][hapmap]
rs9311403	0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs936177	0.82[YRI][hapmap]
rs936180	0.81[YRI][hapmap]
rs936181	0.82[YRI][hapmap]
rs936182	0.80[YRI][hapmap]
rs936186	0.95[YRI][hapmap]
rs9812878	0.84[ASN][1000 genomes]
rs9818382	0.82[ASN][1000 genomes]
rs9821119	0.81[ASN][1000 genomes]
rs9828473	0.90[YRI][hapmap]
rs9837343	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs9843075	0.90[ASN][1000 genomes]
rs9844122	0.87[ASN][1000 genomes]
rs9845728	0.87[ASN][1000 genomes]
rs9854790	0.86[ASN][1000 genomes]
rs9858443	0.86[ASN][1000 genomes]
rs9875235	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
6	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
7	nsv1002970	chr3:47120592-47170607	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv590210	chr3:47126543-47214122	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	esv2581828	chr3:47129901-47129903	Weak transcription Strong transcription Enhancers	n/a	n/a	inside rSNPs	diseases
10	esv2186593	chr3:47129901-47129904	Weak transcription Strong transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12631730	CCDC12	cis	parietal	SCAN
rs12631730	FYCO1	cis	parietal	SCAN
rs12631730	H1FOO	trans	parietal	SCAN
rs12631730	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs12631730	DHX30	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47078000-47130600	Weak transcription	Stomach Mucosa	stomach
2	chr3:47083200-47135200	Weak transcription	Small Intestine	intestine
3	chr3:47083400-47138600	Weak transcription	Psoas Muscle	Psoas
4	chr3:47098800-47149600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:47101400-47147800	Strong transcription	Dnd41	blood
6	chr3:47110200-47150200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:47110400-47133200	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr3:47110600-47131600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:47110600-47148000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:47111000-47147600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:47111800-47132400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:47112400-47153600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:47114600-47147800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:47114800-47137600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:47115400-47131400	Strong transcription	HSMM	muscle
16	chr3:47115400-47147800	Strong transcription	Fetal Thymus	thymus
17	chr3:47117200-47131600	Strong transcription	Liver	Liver
18	chr3:47117200-47133000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:47117600-47131800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:47117600-47148600	Strong transcription	Placenta	Placenta
21	chr3:47118200-47130600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:47118200-47131600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:47118200-47139200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:47118200-47148600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:47118400-47140600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:47118600-47143400	Weak transcription	Fetal Heart	heart
27	chr3:47119200-47131600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:47120200-47135600	Weak transcription	A549	lung
29	chr3:47120800-47131400	Strong transcription	Primary T cells from cord blood	blood
30	chr3:47120800-47131600	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr3:47120800-47131800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:47121600-47132400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:47121600-47133800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:47121800-47130000	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr3:47121800-47131200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:47121800-47131600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:47121800-47131800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:47122600-47143600	Weak transcription	Right Ventricle	heart
39	chr3:47122800-47138800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:47123000-47136000	Weak transcription	HSMMtube	muscle
41	chr3:47123000-47159200	Weak transcription	Brain Substantia Nigra	brain
42	chr3:47124600-47137600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:47124600-47154400	Weak transcription	Fetal Brain Male	brain
44	chr3:47124800-47138600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:47125600-47131600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:47125600-47140600	Strong transcription	Primary B cells from cord blood	blood
47	chr3:47125600-47154600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:47125800-47130600	Weak transcription	Pancreas	Pancrea
49	chr3:47125800-47133800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:47125800-47134400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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