Variant report

Variant	rs2568025
Chromosome Location	chr11:8859384-8859385
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	RCOR1	chr11:8859305-8862295	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8856465..8859459-chr11:8859495..8861215,2	MCF-7	breast:

Variant related genes	Relation type
ST5	TF binding region
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10743091	0.92[ASN][1000 genomes]
rs10840135	0.86[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs11042097	0.81[EUR][1000 genomes]
rs11042098	0.80[EUR][1000 genomes]
rs11042104	0.84[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs16906256	0.84[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs2292049	0.91[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.94[ASN][1000 genomes]
rs2316863	0.86[LWK][hapmap]
rs2568031	0.84[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2568032	0.83[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2568090	0.84[CHD][hapmap]
rs2653569	0.86[MEX][hapmap]
rs34874636	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4929918	0.86[LWK][hapmap]
rs61876202	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7131166	0.83[ASW][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap]
rs7948452	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2568025	WEE1	cis	parietal	SCAN
rs2568025	CYB5R2	cis	parietal	SCAN
rs2568025	PRKCDBP	cis	parietal	SCAN
rs2568025	TMEM9B-AS1	cis	Muscle Skeletal	GTEx
rs2568025	MMP26	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8833200-8859800	Weak transcription	Aorta	Aorta
2	chr11:8845800-8860000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr11:8851000-8861400	Weak transcription	Brain Substantia Nigra	brain
4	chr11:8851800-8862400	Enhancers	Placenta	Placenta
5	chr11:8852800-8861600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr11:8853000-8861400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:8854400-8861000	Weak transcription	Pancreas	Pancrea
8	chr11:8854600-8859400	Weak transcription	Right Atrium	heart
9	chr11:8854600-8859400	Weak transcription	Stomach Mucosa	stomach
10	chr11:8854600-8860000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr11:8854600-8860400	Weak transcription	Gastric	stomach
12	chr11:8854600-8861000	Weak transcription	Lung	lung
13	chr11:8854600-8861400	Weak transcription	A549	lung
14	chr11:8854800-8859400	Weak transcription	Ovary	ovary
15	chr11:8854800-8860600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:8854800-8861000	Weak transcription	Fetal Intestine Small	intestine
17	chr11:8855200-8859800	Weak transcription	Fetal Kidney	kidney
18	chr11:8855400-8859600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr11:8855400-8859800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:8855400-8861000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:8855400-8861000	Weak transcription	Esophagus	oesophagus
22	chr11:8855400-8861000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr11:8855400-8861800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr11:8855600-8859400	Weak transcription	Left Ventricle	heart
25	chr11:8855600-8859600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:8855600-8859800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr11:8855600-8859800	Weak transcription	Fetal Heart	heart
28	chr11:8855600-8860000	Weak transcription	Right Ventricle	heart
29	chr11:8855600-8861200	Weak transcription	Hela-S3	cervix
30	chr11:8855800-8859400	Weak transcription	Spleen	Spleen
31	chr11:8855800-8859800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr11:8855800-8859800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr11:8855800-8861200	Weak transcription	GM12878-XiMat	blood
34	chr11:8855800-8861600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr11:8856000-8859800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr11:8856000-8859800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr11:8856000-8860000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr11:8856200-8859400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:8856200-8859400	Weak transcription	HMEC	breast
40	chr11:8856200-8859800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr11:8856200-8859800	Weak transcription	Colon Smooth Muscle	Colon
42	chr11:8856200-8860000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr11:8856200-8860200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr11:8856200-8860600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr11:8856200-8861200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:8856400-8859400	Weak transcription	Fetal Muscle Leg	muscle
47	chr11:8856400-8859400	Weak transcription	HSMM	muscle
48	chr11:8856400-8859400	Weak transcription	HSMMtube	muscle
49	chr11:8856400-8859400	Weak transcription	Osteobl	bone
50	chr11:8856400-8859600	Weak transcription	Muscle Satellite Cultured Cells	--

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