Variant report

Variant	rs1014228
Chromosome Location	chr3:47652639-47652640
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr3:47652487-47652687	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47652393..47654345-chr3:47713182..47715815,2	K562	blood:
2	chr3:47644023..47648902-chr3:47649054..47653658,7	K562	blood:
3	chr3:47652301..47655679-chr3:47656757..47659038,4	K562	blood:

Variant related genes	Relation type
SMARCC1	TF binding region
ENSG00000214773	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10865948	0.84[CEU][hapmap];0.85[YRI][hapmap];0.90[EUR][1000 genomes]
rs11130138	0.94[ASW][hapmap];0.85[CEU][hapmap];0.98[GIH][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs11130139	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130143	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11130144	0.96[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11130145	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11130146	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11130148	0.96[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap]
rs11712152	0.86[EUR][1000 genomes]
rs11712464	0.96[CEU][hapmap];0.83[GIH][hapmap];0.89[TSI][hapmap]
rs11716582	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11929303	0.95[EUR][1000 genomes]
rs12489865	0.94[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12492915	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12495204	0.88[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap]
rs12497921	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12498027	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12633604	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12635438	0.96[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap]
rs12636198	0.91[EUR][1000 genomes]
rs12636863	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13061412	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs13063042	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs13069142	0.88[EUR][1000 genomes]
rs13081356	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13084555	0.82[EUR][1000 genomes]
rs13085978	0.96[EUR][1000 genomes]
rs13091913	0.96[CEU][hapmap];0.98[GIH][hapmap];0.87[TSI][hapmap]
rs13094264	0.96[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap]
rs1403578	1.00[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1403579	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1464614	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1486915	0.96[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap]
rs17079785	0.83[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap]
rs2047559	0.96[CEU][hapmap];0.96[YRI][hapmap]
rs2049300	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2049301	0.81[EUR][1000 genomes]
rs2133601	0.94[ASW][hapmap];0.89[CEU][hapmap];0.98[GIH][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap]
rs2140335	0.96[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2280567	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293226	0.94[ASW][hapmap];0.96[CEU][hapmap];0.96[GIH][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2351248	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs2882611	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs34252990	0.91[EUR][1000 genomes]
rs34616865	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35167544	0.84[EUR][1000 genomes]
rs35664069	0.81[EUR][1000 genomes]
rs36033865	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732530	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755637	0.96[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs3755638	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs3772403	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4274776	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4858801	0.88[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4858803	0.85[AFR][1000 genomes]
rs4858836	0.83[EUR][1000 genomes]
rs4858842	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4858846	0.96[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4858851	0.96[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap]
rs56746603	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs60110914	0.90[EUR][1000 genomes]
rs60322343	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61620099	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs61675361	0.98[EUR][1000 genomes]
rs6442072	0.92[EUR][1000 genomes]
rs6442074	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6442082	0.88[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap]
rs6768699	0.88[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap]
rs6772301	0.96[CEU][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs6773467	0.81[EUR][1000 genomes]
rs6773732	0.81[EUR][1000 genomes]
rs6774170	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6776963	0.92[CEU][hapmap];0.83[GIH][hapmap];0.89[TSI][hapmap]
rs6777632	0.96[CEU][hapmap];0.96[YRI][hapmap]
rs6784946	0.81[EUR][1000 genomes]
rs6785031	0.82[EUR][1000 genomes]
rs6785669	1.00[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap]
rs6786001	0.88[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap]
rs6789835	0.83[EUR][1000 genomes]
rs6792497	0.96[CEU][hapmap];0.96[YRI][hapmap]
rs6806860	0.83[ASW][hapmap];0.88[CEU][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap]
rs7429162	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs7613934	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7618758	0.88[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs7621236	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7624474	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7631950	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7638103	0.96[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap]
rs7642691	0.83[EUR][1000 genomes]
rs7645846	0.95[CEU][hapmap];0.96[YRI][hapmap]
rs868255	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs869508	0.96[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs870622	1.00[CEU][hapmap];0.82[YRI][hapmap];0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs883661	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs883662	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs883663	0.96[CEU][hapmap];0.98[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs9681917	0.96[CEU][hapmap];0.98[GIH][hapmap];0.87[TSI][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	esv1835200	chr3:47642233-47654375	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1014228	NME6	cis	Esophagus Muscularis	GTEx
rs1014228	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs1014228	MRPS18AP1	cis	lung	GTEx
rs1014228	ZNF589	cis	Nerve Tibial	GTEx
rs1014228	MRPS18AP1	cis	Nerve Tibial	GTEx
rs1014228	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs1014228	DHX30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47621000-47653400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:47622600-47653400	Weak transcription	Stomach Mucosa	stomach
3	chr3:47623400-47655000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:47624000-47653200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:47626200-47698600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:47626400-47655600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:47626400-47680600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:47626600-47688600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:47626600-47699800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:47626800-47680800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr3:47632400-47652800	Weak transcription	Aorta	Aorta
12	chr3:47632400-47658600	Weak transcription	A549	lung
13	chr3:47632400-47660800	Weak transcription	Esophagus	oesophagus
14	chr3:47634200-47661000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:47635000-47686800	Strong transcription	Dnd41	blood
16	chr3:47636800-47672800	Weak transcription	Small Intestine	intestine
17	chr3:47637200-47665000	Strong transcription	Primary T cells from cord blood	blood
18	chr3:47638000-47681200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:47638200-47665800	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr3:47639200-47653600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:47639200-47654600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:47639200-47655000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr3:47639200-47655200	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:47639200-47655200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:47639200-47655600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:47639200-47675800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:47641800-47655800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:47642800-47653600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:47643600-47653600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:47643600-47684800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:47643800-47666400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:47644000-47654000	Strong transcription	Fetal Thymus	thymus
33	chr3:47644200-47676000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr3:47644400-47654200	Strong transcription	Primary B cells from cord blood	blood
35	chr3:47644400-47655200	Strong transcription	GM12878-XiMat	blood
36	chr3:47644400-47664600	Strong transcription	Duodenum Mucosa	Duodenum
37	chr3:47644600-47663800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:47645000-47656600	Strong transcription	K562	blood
39	chr3:47645200-47652800	Strong transcription	Placenta	Placenta
40	chr3:47645200-47653600	Strong transcription	Fetal Muscle Trunk	muscle
41	chr3:47645200-47654200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:47645200-47663200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:47645400-47656800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:47645400-47663600	Strong transcription	HepG2	liver
45	chr3:47645600-47654000	Strong transcription	Liver	Liver
46	chr3:47645800-47664600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr3:47646600-47658600	Strong transcription	Fetal Brain Female	brain
48	chr3:47646600-47666600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:47646800-47653200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:47646800-47653800	Strong transcription	Brain Germinal Matrix	brain

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