Variant report

Variant	rs11604680
Chromosome Location	chr11:47457539-47457540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47457446..47459034-chr11:47462539..47464342,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165917	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1057233	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs1064608	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10742803	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10769258	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs10769262	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs10838698	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs10838699	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs10838704	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10838706	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10838708	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10838724	0.88[ASN][1000 genomes]
rs11039199	0.84[AFR][1000 genomes]
rs11039200	0.87[AFR][1000 genomes]
rs11039212	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs11039219	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039238	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039255	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11039265	0.85[ASN][1000 genomes]
rs11570094	0.84[CEU][hapmap]
rs11600581	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11601603	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs11605672	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[EUR][1000 genomes]
rs11607981	0.81[EUR][1000 genomes]
rs12146565	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12419692	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12798346	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12802273	0.81[EUR][1000 genomes]
rs12803525	0.82[EUR][1000 genomes]
rs1317149	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1317164	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2053979	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2053980	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2071304	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs2293577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2293578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293580	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2868459	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34958982	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs35184771	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35496532	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35705029	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3740689	1.00[YRI][hapmap]
rs3781624	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3781625	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3781626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3781627	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3817334	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3817335	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4752832	0.83[ASN][1000 genomes]
rs4752838	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752845	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4752856	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4752857	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4752990	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes]
rs4752993	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs4752994	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs4752999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4992357	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs55677087	0.81[EUR][1000 genomes]
rs55876153	0.82[EUR][1000 genomes]
rs55927797	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56030824	0.83[EUR][1000 genomes]
rs58965622	0.83[EUR][1000 genomes]
rs60075622	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6485753	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs6485756	0.83[ASN][1000 genomes]
rs67472071	0.80[EUR][1000 genomes]
rs7106956	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7107726	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7124681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs755553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs755554	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs755555	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7924485	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7925389	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7928842	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7937331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7940536	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs896816	1.00[CEU][hapmap];0.90[CHB][hapmap]

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	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	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
3	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
4	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
5	nsv975328	chr11:47446815-47471052	Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11604680	SPI1	cis	Lymphoblastoid	GTEx
rs11604680	Hs.6637	cis	multi-tissue	Pritchard
rs11604680	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs11604680	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs11604680	C1QTNF4	cis	Whole Blood	GTEx
rs11604680	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs11604680	C1QTNF4	cis	multi-tissue	Pritchard
rs11604680	C1QTNF4	cis	Muscle Skeletal	GTEx
rs11604680	SPI1	cis	multi-tissue	Pritchard
rs11604680		cis	Lymphoblastoid	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47448600-47459600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:47448600-47488400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:47449000-47459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:47449000-47459400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:47453400-47458800	Enhancers	HepG2	liver
6	chr11:47453400-47469200	Weak transcription	Psoas Muscle	Psoas
7	chr11:47453400-47480000	Weak transcription	Thymus	Thymus
8	chr11:47453600-47459000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr11:47454600-47457800	Enhancers	Liver	Liver
10	chr11:47455000-47458400	Weak transcription	Fetal Intestine Small	intestine
11	chr11:47455200-47458800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:47455200-47459000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr11:47455200-47459200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr11:47455200-47459400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:47456200-47458800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr11:47456200-47459200	Weak transcription	Adipose Nuclei	Adipose
17	chr11:47456400-47458800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr11:47456400-47459000	Weak transcription	Brain Anterior Caudate	brain
19	chr11:47456400-47460200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:47456400-47460400	Weak transcription	HSMMtube	muscle
21	chr11:47456600-47458800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:47456600-47459000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:47456600-47459000	Weak transcription	Fetal Muscle Leg	muscle
24	chr11:47456600-47459200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:47456600-47463600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:47456600-47468600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr11:47457200-47457800	Enhancers	Spleen	Spleen
28	chr11:47457200-47457800	Enhancers	HSMM	muscle
29	chr11:47457200-47458000	ZNF genes & repeats	Right Atrium	heart
30	chr11:47457400-47480200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr11:47457400-47480800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:47457400-47488400	Weak transcription	Gastric	stomach

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