Variant report

Variant	rs1783827
Chromosome Location	chr11:57409538-57409539
allele	A/G
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	CTCF	chr11:57409440-57409590	GM12868	blood:	n/a	n/a
2	POLR2A	chr11:57406679-57409638	PBDE	blood:	n/a	n/a
3	POLR2A	chr11:57404829-57418710	PFSK-1	brain:	n/a	n/a
4	CTCF	chr11:57409400-57409550	AG04449	skin:	n/a	n/a
5	POLR2A	chr11:57404853-57409799	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr11:57404978-57410762	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:57404927-57409727	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr11:57409440-57409590	HPAF	blood vessel:	n/a	n/a
9	CTCF	chr11:57408232-57409596	A549	lung:	n/a	chr11:57409157-57409178 chr11:57409163-57409179 chr11:57409162-57409180
10	POLR2A	chr11:57408728-57409613	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr11:57404802-57417187	SK-N-MC	brain:	n/a	n/a
12	CTCF	chr11:57409400-57409550	NHLF	lung:	n/a	n/a
13	ATF2	chr11:57408370-57409591	H1-hESC	embryonic stem cell:	n/a	n/a
14	RAD21	chr11:57408876-57409583	SK-N-SH	brain:	n/a	chr11:57409160-57409179
15	CTCF	chr11:57408367-57409579	HCT-116	colon:	n/a	chr11:57409157-57409178 chr11:57409163-57409179 chr11:57409162-57409180
16	CTCF	chr11:57409500-57409650	HVMF	connective:	n/a	n/a
17	CTCF	chr11:57409460-57409610	GM12867	blood:	n/a	n/a
18	POLR2A	chr11:57405031-57409669	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr11:57409126-57409588	HepG2	liver:	n/a	n/a
20	CTCF	chr11:57409440-57409590	GM06990	blood:	n/a	n/a
21	CTCF	chr11:57409520-57409670	HCFaa	heart:	n/a	n/a
22	CTCF	chr11:57408341-57409607	SK-N-SH	brain:	n/a	chr11:57409157-57409178 chr11:57409163-57409179 chr11:57409162-57409180
23	SMC3	chr11:57408359-57409756	SK-N-SH	brain:	n/a	chr11:57409164-57409178
24	POLR2A	chr11:57408996-57409649	ECC-1	luminal epithelium:	n/a	n/a
25	CTCF	chr11:57409460-57409610	AG10803	skin:	n/a	n/a
26	CTCF	chr11:57409431-57409558	GM12892	blood:	n/a	n/a
27	POLR2A	chr11:57408982-57409677	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr11:57404949-57409673	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:57405566..57408530-chr11:57408605..57410550,2	MCF-7	breast:
2	chr11:57335324..57336323-chr11:57408291..57409695,14	MCF-7	breast:
3	chr11:57409445..57411077-chr11:57414128..57416873,2	K562	blood:
4	chr11:57334539..57338384-chr11:57406664..57411574,5	MCF-7	breast:
5	chr11:57224546..57225432-chr11:57408726..57409938,3	K562	blood:
6	chr11:57335355..57336298-chr11:57408531..57409635,7	K562	blood:
7	chr11:57293312..57295959-chr11:57408961..57411007,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254602	TF binding region
ENSG00000166793	Chromatin interaction
ENSG00000254602	Chromatin interaction
ENSG00000156587	Chromatin interaction
ENSG00000172409	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10792110	0.89[JPT][hapmap]
rs10896644	1.00[JPT][hapmap]
rs10896649	0.89[JPT][hapmap]
rs11229109	0.80[CEU][hapmap];0.89[JPT][hapmap]
rs11570176	1.00[JPT][hapmap]
rs11570181	1.00[JPT][hapmap]
rs1613592	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1631684	0.82[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1647394	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1647403	0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17455422	1.00[JPT][hapmap]
rs1783826	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1783828	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783829	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1783978	1.00[JPT][hapmap]
rs1783979	1.00[JPT][hapmap]
rs1783980	0.89[JPT][hapmap]
rs1783981	0.89[JPT][hapmap]
rs1783983	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1783984	0.88[AMR][1000 genomes]
rs1783985	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1785498	0.88[JPT][hapmap]
rs1798172	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1798173	0.81[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1798177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2156638	0.89[JPT][hapmap]
rs2956981	1.00[JPT][hapmap]
rs3017889	1.00[JPT][hapmap]
rs36036499	1.00[JPT][hapmap]
rs4611222	0.89[JPT][hapmap]
rs627145	1.00[JPT][hapmap]
rs653889	1.00[JPT][hapmap]
rs665058	1.00[JPT][hapmap]
rs7117020	1.00[JPT][hapmap]
rs7120868	1.00[JPT][hapmap]
rs7947357	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs929934	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	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
6	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
7	esv992553	chr11:57408294-57419351	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1783827	YPEL4	cis	lung	GTEx
rs1783827	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs1783827	TIMM10	cis	Esophagus Mucosa	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57403000-57412200	Weak transcription	Hela-S3	cervix
2	chr11:57406800-57409600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr11:57407200-57412200	Weak transcription	Ovary	ovary
4	chr11:57407400-57412600	Weak transcription	GM12878-XiMat	blood
5	chr11:57407600-57412200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr11:57407600-57412200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr11:57407600-57412200	Weak transcription	Spleen	Spleen
8	chr11:57407600-57413000	Weak transcription	Right Ventricle	heart
9	chr11:57407600-57413200	Weak transcription	Esophagus	oesophagus
10	chr11:57407800-57409600	Enhancers	Fetal Heart	heart
11	chr11:57407800-57409600	Genic enhancers	Fetal Lung	lung
12	chr11:57407800-57409600	Enhancers	Dnd41	blood
13	chr11:57407800-57412200	Weak transcription	Pancreas	Pancrea
14	chr11:57408000-57409600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:57408000-57412000	Weak transcription	Colon Smooth Muscle	Colon
16	chr11:57408000-57412200	Weak transcription	Lung	lung
17	chr11:57408200-57409600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr11:57408200-57409600	Enhancers	Fetal Thymus	thymus
19	chr11:57408200-57410600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:57408200-57411200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:57408200-57411200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr11:57408200-57411400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr11:57408200-57411400	Genic enhancers	Fetal Muscle Leg	muscle
24	chr11:57408200-57412000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr11:57408200-57412000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:57408400-57409600	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:57408400-57410600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:57408400-57412200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:57408600-57409600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr11:57408600-57409600	Enhancers	Brain Germinal Matrix	brain
31	chr11:57408600-57410400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr11:57408600-57411200	Weak transcription	NHEK	skin
33	chr11:57408800-57409600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:57408800-57409600	Genic enhancers	HSMM	muscle
35	chr11:57408800-57409600	Genic enhancers	NHDF-Ad	bronchial
36	chr11:57408800-57410200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:57408800-57410600	Weak transcription	Placenta	Placenta
38	chr11:57408800-57411600	Genic enhancers	H1 Cell Line	embryonic stem cell
39	chr11:57408800-57411800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr11:57408800-57412000	Weak transcription	Left Ventricle	heart
41	chr11:57408800-57412000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr11:57408800-57412000	Weak transcription	Right Atrium	heart
43	chr11:57408800-57412200	Weak transcription	Adipose Nuclei	Adipose
44	chr11:57408800-57412200	Weak transcription	Brain Hippocampus Middle	brain
45	chr11:57408800-57412200	Weak transcription	Thymus	Thymus
46	chr11:57408800-57412600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr11:57408800-57412600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:57408800-57413400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr11:57409000-57409600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:57409000-57409600	Genic enhancers	iPS-15b Cell Line	embryonic stem cell

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