Variant report

Variant	rs56392705
Chromosome Location	chr11:57518392-57518393
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	POLR2A	chr11:57518372-57518398	MCF10A-Er-Src	breast:	n/a	n/a
2	MAFK	chr11:57518390-57518601	HepG2	liver:	n/a	chr11:57518443-57518458 chr11:57518443-57518459 chr11:57518442-57518456 chr11:57518443-57518454

No.	Distal block	Cell Line	Cell type
1	chr11:57508102..57510467-chr11:57518136..57520066,2	MCF-7	breast:
2	chr11:57507833..57511012-chr11:57515890..57519512,4	MCF-7	breast:
3	chr11:57517755..57521184-chr11:57545638..57549281,5	MCF-7	breast:
4	chr11:57516743..57518799-chr11:57520636..57522160,2	MCF-7	breast:
5	chr11:57517655..57520896-chr11:57569162..57571225,3	MCF-7	breast:

Variant related genes	Relation type
CTNND1	TF binding region
ENSG00000254732	Chromatin interaction
ENSG00000198561	Chromatin interaction
ENSG00000211450	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10750870	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10792110	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896644	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10896649	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10896653	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11229109	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11229119	0.84[AMR][1000 genomes]
rs11570176	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11570181	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12270209	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12274865	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12363024	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12805343	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1424753	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1613592	0.82[ASN][1000 genomes]
rs1624389	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1647403	0.82[ASN][1000 genomes]
rs17455422	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17455626	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783818	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1783824	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783976	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783977	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1783978	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783979	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783980	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783981	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783985	0.82[ASN][1000 genomes]
rs1785498	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1785499	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1786438	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1798172	0.82[ASN][1000 genomes]
rs1798173	0.82[ASN][1000 genomes]
rs2156638	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2911728	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2956981	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956982	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3017889	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36036499	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4611222	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs471398	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs547118	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs585337	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs585761	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588612	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs593239	0.81[ASN][1000 genomes]
rs606499	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs623541	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs627145	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs639158	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs644219	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs645145	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs652191	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs652908	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs653889	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs658936	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs659165	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs665058	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs671508	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs682258	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs686489	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7105506	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7115528	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7117020	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7120868	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7479922	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7948571	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56392705	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs56392705	YPEL4	cis	lung	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57509800-57519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:57510200-57518400	Weak transcription	Psoas Muscle	Psoas
3	chr11:57510400-57519000	Weak transcription	Stomach Mucosa	stomach
4	chr11:57510400-57519400	Weak transcription	Right Atrium	heart
5	chr11:57510400-57519400	Weak transcription	Small Intestine	intestine
6	chr11:57510400-57528800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr11:57511800-57519400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:57511800-57528800	Weak transcription	Fetal Brain Male	brain
9	chr11:57512000-57528800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:57512200-57528800	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:57512400-57519000	Weak transcription	HepG2	liver
12	chr11:57512400-57519400	Weak transcription	HUVEC	blood vessel
13	chr11:57512400-57520800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:57512400-57528800	Weak transcription	HSMM	muscle
15	chr11:57512600-57518600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr11:57512600-57519000	Weak transcription	A549	lung
17	chr11:57512600-57519400	Weak transcription	Ovary	ovary
18	chr11:57512600-57519400	Weak transcription	Pancreas	Pancrea
19	chr11:57512600-57519400	Weak transcription	HMEC	breast
20	chr11:57512600-57521800	Weak transcription	Fetal Lung	lung
21	chr11:57512600-57526400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr11:57512600-57528800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr11:57512800-57521600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr11:57512800-57528800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:57513000-57518600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr11:57513000-57528800	Weak transcription	HSMMtube	muscle
27	chr11:57513200-57519400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:57513200-57528600	Weak transcription	NHEK	skin
29	chr11:57513600-57519000	Weak transcription	NHLF	lung
30	chr11:57513600-57519200	Weak transcription	Brain Substantia Nigra	brain
31	chr11:57513600-57519400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr11:57513600-57519400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr11:57513600-57519400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr11:57513600-57519400	Weak transcription	Brain Hippocampus Middle	brain
35	chr11:57513600-57519400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr11:57513600-57519400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr11:57513600-57520200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr11:57513600-57520200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr11:57513600-57528800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr11:57513600-57528800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr11:57513600-57528800	Weak transcription	Colonic Mucosa	Colon
42	chr11:57513600-57529200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:57513600-57531200	Weak transcription	Gastric	stomach
44	chr11:57513800-57518600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:57513800-57518600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:57513800-57519400	Weak transcription	Duodenum Mucosa	Duodenum
47	chr11:57513800-57519400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr11:57513800-57519400	Weak transcription	Right Ventricle	heart
49	chr11:57513800-57519400	Weak transcription	GM12878-XiMat	blood
50	chr11:57513800-57520400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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