Variant report

Variant	rs470392
Chromosome Location	chr11:119994421-119994422
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	POLR2A	chr11:119991787-119995121	Hela-S3	cervix:	n/a	n/a
2	ELF1	chr11:119993958-119994423	HepG2	liver:	n/a	chr11:119994206-119994219
3	POLR2A	chr11:119994383-119994920	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr11:119991838-119994802	Hela-S3	cervix:	n/a	n/a
5	SMARCC1	chr11:119991833-119996186	Hela-S3	cervix:	n/a	chr11:119993842-119993851 chr11:119995853-119995862 chr11:119993841-119993850 chr11:119994713-119994722
6	ELF1	chr11:119994024-119994447	GM12878	blood:	n/a	chr11:119994206-119994219
7	CBX3	chr11:119993953-119994441	K562	blood:	n/a	n/a
8	POLR2A	chr11:119994378-119994599	MCF10A-Er-Src	breast:	n/a	n/a
9	GTF2F1	chr11:119993620-119994523	Hela-S3	cervix:	n/a	n/a
10	ELF1	chr11:119993939-119994459	K562	blood:	n/a	chr11:119994206-119994219
11	POLR2A	chr11:119993507-119994759	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:119992602..119994710-chr11:119998240..120000665,2	MCF-7	breast:
2	chr11:119988388..119990806-chr11:119992979..119995049,2	MCF-7	breast:
3	chr11:119993537..119997499-chr11:119998076..120003019,6	K562	blood:
4	chr11:119992107..119994567-chr11:120009192..120013001,3	MCF-7	breast:
5	chr11:119992154..119994463-chr11:120170248..120173038,2	MCF-7	breast:
6	chr11:119598280..119601010-chr11:119990751..119994590,4	MCF-7	breast:

Variant related genes	Relation type
TRIM29	TF binding region
ENSG00000137699	Chromatin interaction
ENSG00000254854	Chromatin interaction
ENSG00000137709	Chromatin interaction
ENSG00000110400	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs470941	0.86[CHB][hapmap]
rs530294	0.91[ASN][1000 genomes]
rs550164	0.86[CHB][hapmap]
rs590843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs606970	0.89[YRI][hapmap]
rs670855	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1050132	chr11:119976310-120010437	Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs470392	THY1	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119991200-119996600	Enhancers	Placenta	Placenta
2	chr11:119991200-119997000	Enhancers	Placenta Amnion	Placenta Amnion
3	chr11:119991200-119999000	Genic enhancers	HMEC	breast
4	chr11:119991400-119996000	Enhancers	Stomach Mucosa	stomach
5	chr11:119992200-119994800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:119992600-119994600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr11:119993000-119994600	Enhancers	Fetal Intestine Large	intestine
8	chr11:119993200-119995200	Flanking Active TSS	Hela-S3	cervix
9	chr11:119993400-119998800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr11:119993400-119998800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:119993400-119999800	Weak transcription	Fetal Thymus	thymus
12	chr11:119993400-120000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:119993600-119994600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:119993600-119994800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:119993600-119995800	Genic enhancers	NHEK	skin
16	chr11:119993600-119996000	Enhancers	K562	blood
17	chr11:119993800-119994600	Bivalent Enhancer	HepG2	liver
18	chr11:119993800-119996800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:119993800-119996800	Genic enhancers	Esophagus	oesophagus
20	chr11:119993800-120001800	Weak transcription	Pancreas	Pancrea
21	chr11:119994200-119994600	Enhancers	Spleen	Spleen
22	chr11:119994200-119996000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr11:119994200-119997600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr11:119994400-119995000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:119994400-119996200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:119994400-119996800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr11:119994400-119998800	Weak transcription	Duodenum Mucosa	Duodenum

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