Variant report

Variant	rs12574047
Chromosome Location	chr11:73805889-73805890
allele	G/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	GATA3	chr11:73805498-73805965	T-47D	breast:	n/a	n/a
2	RAD21	chr11:73805404-73805915	MCF-7	breast:	n/a	n/a
3	CTCF	chr11:73805391-73805949	HCT-116	colon:	n/a	n/a
4	RAD21	chr11:73805410-73805911	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:73706788..73709340-chr11:73804730..73807192,2	MCF-7	breast:
2	chr11:73805096..73806451-chr11:73937582..73938571,3	MCF-7	breast:
3	chr11:73805175..73806067-chr11:73937886..73938551,2	MCF-7	breast:

Variant related genes	Relation type
C2CD3	TF binding region
ENSG00000256723	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10219237	0.87[TSI][hapmap]
rs10431176	0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10501415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10898955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10898957	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898958	0.85[ASN][1000 genomes]
rs10898959	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10898960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10898961	1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs10898962	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10898963	1.00[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs10898966	0.89[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap]
rs10898975	0.87[CHD][hapmap]
rs11235971	0.91[GIH][hapmap]
rs11235972	0.90[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap]
rs11235988	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11235994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11235995	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235997	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235998	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11235999	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236002	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11236003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11236005	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11236016	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11236018	0.84[EUR][1000 genomes]
rs11236020	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11236026	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11236027	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11236029	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11236042	0.87[CHD][hapmap]
rs11600314	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]
rs11601582	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11602451	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap];0.82[ASN][1000 genomes]
rs11603981	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11604125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11604713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11606804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11607335	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11608147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12222213	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12223320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12574038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12574039	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];1.00[ASN][1000 genomes]
rs12574556	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12574650	0.82[ASN][1000 genomes]
rs12574824	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12574898	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12574960	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12575211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1405653	0.82[ASN][1000 genomes]
rs1405654	0.82[ASN][1000 genomes]
rs1474471	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1527302	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1615607	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1685333	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap]
rs17132701	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17132715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800006	0.89[CHB][hapmap]
rs1800849	0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap]
rs1944971	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap]
rs2091436	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2178000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2282488	0.87[CHD][hapmap]
rs35826958	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3741132	0.87[CHD][hapmap]
rs3741133	0.89[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap]
rs3741135	0.91[GIH][hapmap]
rs3814724	1.00[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs4019299	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4537786	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4539349	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4565925	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55823944	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56298621	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56366246	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57117016	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59109060	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59605334	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60834556	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61901208	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61901211	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61901216	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61901238	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61901245	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61901246	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61901247	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61901248	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61901252	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61902362	0.80[ASN][1000 genomes]
rs6592547	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7110734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7115146	0.81[ASN][1000 genomes]
rs7115407	0.86[CEU][hapmap];0.93[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7117465	0.87[CHD][hapmap]
rs7119710	0.86[CEU][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7125032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7125400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72341762	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7930460	0.91[GIH][hapmap]
rs7935920	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7941203	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7941525	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7949639	0.84[CHB][hapmap]
rs7951239	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7951290	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7951743	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7952669	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs826035	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs826044	0.93[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs826057	0.81[YRI][hapmap]
rs826058	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	esv3406283	chr11:73805531-73806190	Strong transcription Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12574047	PPME1	cis	cerebellum	SCAN
rs12574047	FAM168A	cis	parietal	SCAN
rs12574047	P4HA3	cis	cerebellum	SCAN
rs12574047	STARD10	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73777600-73818600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr11:73781800-73849200	Weak transcription	Stomach Mucosa	stomach
3	chr11:73782600-73823800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:73785600-73823600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:73787800-73811400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:73794600-73823600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:73794800-73806600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:73794800-73806600	Strong transcription	Fetal Lung	lung
9	chr11:73795000-73806000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:73795000-73806000	Strong transcription	Brain Anterior Caudate	brain
11	chr11:73795000-73806400	Strong transcription	Adipose Nuclei	Adipose
12	chr11:73795000-73806600	Strong transcription	Fetal Muscle Leg	muscle
13	chr11:73795000-73808600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:73795000-73817400	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr11:73795000-73817600	Strong transcription	Primary B cells from cord blood	blood
16	chr11:73795200-73806000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:73795200-73806000	Strong transcription	Placenta	Placenta
18	chr11:73795200-73806400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr11:73795200-73806400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:73795200-73806400	Strong transcription	HSMMtube	muscle
21	chr11:73795200-73806600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr11:73795200-73807200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr11:73795200-73814600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr11:73795200-73814600	Strong transcription	Left Ventricle	heart
25	chr11:73795200-73814800	Strong transcription	Liver	Liver
26	chr11:73795200-73815200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr11:73795200-73817600	Strong transcription	Primary T cells from cord blood	blood
28	chr11:73795200-73817600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr11:73795200-73818200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:73795200-73820600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr11:73795200-73823800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr11:73795400-73817800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr11:73795600-73806000	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr11:73795800-73806400	Strong transcription	Fetal Brain Female	brain
35	chr11:73795800-73806600	Strong transcription	Hela-S3	cervix
36	chr11:73795800-73815000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:73795800-73817800	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr11:73796000-73807600	Strong transcription	Brain Hippocampus Middle	brain
39	chr11:73796000-73817800	Strong transcription	HSMM	muscle
40	chr11:73796600-73806600	Strong transcription	Fetal Intestine Large	intestine
41	chr11:73796800-73806600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:73797000-73806000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:73797000-73812600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:73797000-73813600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr11:73797200-73807400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:73797200-73812600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr11:73797200-73817600	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr11:73797400-73809200	Weak transcription	HepG2	liver
49	chr11:73798000-73806400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr11:73798000-73808000	Weak transcription	Psoas Muscle	Psoas

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