Variant report

Variant	rs11587676
Chromosome Location	chr1:152159961-152159962
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	STAT3	chr1:152159067-152160022	MCF10A-Er-Src	breast:	n/a	chr1:152159613-152159622 chr1:152159611-152159622 chr1:152159612-152159621

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152019527..152021275-chr1:152158923..152161325,2	MCF-7	breast:
2	chr1:152111690..152113718-chr1:152156883..152160461,3	MCF-7	breast:

Variant related genes	Relation type
FLG-AS1	TF binding region
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10749669	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs10749670	0.93[CEU][hapmap]
rs10788824	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs10888470	0.93[CEU][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap]
rs10888471	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs10888473	0.93[CEU][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap]
rs11204947	0.93[CEU][hapmap];0.91[CHD][hapmap];0.90[MEX][hapmap]
rs11204948	0.93[CEU][hapmap];0.91[CHD][hapmap];0.95[MEX][hapmap]
rs11204949	0.85[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs11204978	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11204980	0.93[CEU][hapmap]
rs11204981	0.93[CEU][hapmap];0.91[CHD][hapmap];0.90[MEX][hapmap]
rs11583524	0.93[CEU][hapmap];0.86[CHB][hapmap];0.85[AMR][1000 genomes]
rs11584340	0.93[CEU][hapmap]
rs11584427	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs11586114	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs11588174	0.93[CEU][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap]
rs11589587	0.82[EUR][1000 genomes]
rs11590365	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12405278	0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs12408581	0.82[EUR][1000 genomes]
rs1390488	0.93[CEU][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap]
rs1390490	0.93[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes]
rs1496045	0.93[CEU][hapmap];0.93[CHD][hapmap];0.82[MEX][hapmap]
rs1496049	0.86[AMR][1000 genomes]
rs1858480	0.93[CEU][hapmap]
rs1858482	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap]
rs2065955	1.00[CEU][hapmap]
rs2184953	0.86[CEU][hapmap]
rs2338555	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs3120659	0.93[CEU][hapmap];0.84[CHD][hapmap]
rs3126066	0.93[CEU][hapmap]
rs3126085	0.93[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap]
rs3126088	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs3126091	0.92[CEU][hapmap]
rs4845423	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs4845736	1.00[CEU][hapmap];0.93[CHD][hapmap];0.86[MEX][hapmap]
rs4845745	0.93[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[MEX][hapmap]
rs4845750	0.93[CEU][hapmap];0.90[CHD][hapmap];0.82[MEX][hapmap]
rs55982921	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56013982	0.82[EUR][1000 genomes]
rs6587666	0.93[CEU][hapmap];0.91[CHD][hapmap];0.90[MEX][hapmap]
rs6666382	0.93[CEU][hapmap];0.91[CHD][hapmap];0.90[MEX][hapmap]
rs72696963	0.82[EUR][1000 genomes]
rs7550106	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs877776	0.93[CEU][hapmap]

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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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 target site	196 gene(s)	inside rSNPs	diseases
4	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv872442	chr1:152054120-152187641	Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv547854	chr1:152145661-152165878	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11587676	FLG	cis	Thyroid	GTEx
rs11587676	VPS45	cis	cerebellum	SCAN
rs11587676	IVL	cis	parietal	SCAN
rs11587676	GABPB2	cis	cerebellum	SCAN
rs11587676	S100A9	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152152200-152161200	Weak transcription	Right Atrium	heart
2	chr1:152154000-152160200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:152154400-152161400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:152154600-152160200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:152154600-152160400	Enhancers	Colon Smooth Muscle	Colon
6	chr1:152155600-152160200	Enhancers	NHEK	skin
7	chr1:152156000-152161200	Weak transcription	A549	lung
8	chr1:152156000-152161200	Weak transcription	HSMM	muscle
9	chr1:152157800-152161200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:152158000-152161200	Weak transcription	NHDF-Ad	bronchial
11	chr1:152158200-152160600	Enhancers	Hela-S3	cervix
12	chr1:152158200-152161000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:152158200-152161000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:152158200-152161400	Weak transcription	NH-A	brain
15	chr1:152158600-152161200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:152158800-152161200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:152159000-152161200	Weak transcription	Ovary	ovary
18	chr1:152159400-152160000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:152159800-152161200	Weak transcription	Esophagus	oesophagus
20	chr1:152159800-152161200	Weak transcription	HMEC	breast
21	chr1:152159800-152161200	Weak transcription	Osteobl	bone

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