Variant report

Variant	rs12802273
Chromosome Location	chr11:47418306-47418307
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	chr11:47416151..47418895-chr11:47586699..47588478,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213619	Chromatin interaction
ENSG00000149187	Chromatin interaction
ENSG00000110536	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1057233	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10734557	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10742803	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10769258	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10769262	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838698	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10838699	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838704	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838706	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039195	0.81[EUR][1000 genomes]
rs11039199	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11039200	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11039202	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039203	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039212	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039219	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11600581	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11601603	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11604680	0.81[EUR][1000 genomes]
rs11605672	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607981	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12146565	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12803525	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317164	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1542321	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2053979	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2053980	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2071304	0.81[EUR][1000 genomes]
rs2084946	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2293577	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2293578	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2293580	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2856661	0.81[EUR][1000 genomes]
rs2868459	0.85[EUR][1000 genomes]
rs35496532	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35705029	0.82[EUR][1000 genomes]
rs35996350	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3740686	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3781624	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3781625	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3781626	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3781627	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4752827	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4752832	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4752838	0.81[EUR][1000 genomes]
rs4752987	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4752990	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752993	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752994	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752999	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4992357	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55677087	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55876153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55927797	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56030824	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58965622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60075622	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6485753	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6485756	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67116452	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67472071	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7105851	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7106956	0.83[EUR][1000 genomes]
rs7107726	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7111957	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs755553	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs755554	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs755555	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7924485	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7925299	0.82[AMR][1000 genomes]
rs7928163	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7928419	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7937331	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7940536	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs896815	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs896816	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs935914	0.94[EUR][1000 genomes];0.90[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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv554210	chr11:47380593-47449544	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
8	nsv541034	chr11:47404083-47440081	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
9	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12802273	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs12802273	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs12802273	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs12802273	C1QTNF4	cis	Muscle Skeletal	GTEx
rs12802273	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47399400-47421400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr11:47399800-47421200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr11:47400000-47421200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr11:47410200-47421200	Weak transcription	Fetal Intestine Small	intestine
5	chr11:47414600-47421200	Weak transcription	Stomach Mucosa	stomach
6	chr11:47415200-47421200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:47415400-47419400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:47415400-47419600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:47415400-47421200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:47415400-47421400	Weak transcription	Right Atrium	heart
11	chr11:47415600-47419800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr11:47415600-47421400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:47416200-47419800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr11:47416200-47420000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr11:47416200-47421400	Weak transcription	Liver	Liver
16	chr11:47416400-47422000	Weak transcription	HSMM	muscle
17	chr11:47416600-47419600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:47416600-47419800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:47416600-47421200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:47416600-47421400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:47416600-47421400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:47416800-47419600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr11:47416800-47419800	Weak transcription	Esophagus	oesophagus
24	chr11:47416800-47421200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr11:47416800-47421200	Weak transcription	Osteobl	bone
26	chr11:47416800-47421400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:47416800-47421400	Weak transcription	NH-A	brain
28	chr11:47416800-47421800	Weak transcription	NHLF	lung
29	chr11:47417000-47419600	Weak transcription	K562	blood
30	chr11:47417000-47421200	Weak transcription	Fetal Stomach	stomach
31	chr11:47417000-47421400	Weak transcription	Left Ventricle	heart
32	chr11:47417200-47421000	Enhancers	Primary B cells from peripheral blood	blood
33	chr11:47417200-47421000	Weak transcription	Thymus	Thymus
34	chr11:47417200-47421200	Weak transcription	Right Ventricle	heart
35	chr11:47417200-47421200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr11:47417400-47418400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr11:47417400-47421200	Enhancers	Primary hematopoietic stem cells	blood
38	chr11:47417400-47421200	Weak transcription	Colonic Mucosa	Colon
39	chr11:47417400-47421200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr11:47417400-47421400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:47417600-47418400	Enhancers	Primary B cells from cord blood	blood
42	chr11:47417600-47419000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr11:47417600-47419600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr11:47417600-47420400	Weak transcription	Fetal Muscle Leg	muscle
45	chr11:47417600-47421200	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr11:47417600-47421200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:47417600-47421200	Weak transcription	Brain Anterior Caudate	brain
48	chr11:47417600-47421200	Weak transcription	Brain Substantia Nigra	brain
49	chr11:47417600-47421200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr11:47417600-47421200	Weak transcription	HUVEC	blood vessel

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