Variant report

Variant	rs477557
Chromosome Location	chr11:66387094-66387095
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	SETDB1	chr11:66386744-66387568	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:66356377..66365681-chr11:66380910..66388291,23	K562	blood:
2	chr11:66382408..66387659-chr11:66442901..66446973,11	MCF-7	breast:
3	chr11:66325010..66327957-chr11:66384615..66387418,2	K562	blood:
4	chr11:66358389..66364594-chr11:66381544..66387255,17	MCF-7	breast:

Variant related genes	Relation type
RNU4-39P	TF binding region
ENSG00000182791	Chromatin interaction
ENSG00000173914	Chromatin interaction
ENSG00000250105	Chromatin interaction
ENSG00000173992	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12417769	0.86[ASN][1000 genomes]
rs12577111	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12804382	0.85[ASN][1000 genomes]
rs12805133	0.81[ASN][1000 genomes]
rs1791684	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2276138	0.85[ASN][1000 genomes]
rs34900764	0.83[EUR][1000 genomes]
rs3741363	0.86[ASN][1000 genomes]
rs474602	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs486584	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4930387	0.85[ASN][1000 genomes]
rs498045	0.84[EUR][1000 genomes]
rs503250	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs535211	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs556759	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs577023	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs577335	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs580910	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs692892	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs477557	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs477557	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs477557	ACTN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66383200-66387600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:66384200-66389200	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr11:66385000-66387600	Transcr. at gene 5' and 3'	Hela-S3	cervix
4	chr11:66385000-66387600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr11:66385200-66387600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:66385400-66406200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:66385600-66387600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
8	chr11:66385600-66388800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr11:66385800-66387800	Transcr. at gene 5' and 3'	HMEC	breast
10	chr11:66385800-66388400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:66386000-66387600	Active TSS	Colonic Mucosa	Colon
12	chr11:66386000-66390600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:66386200-66398400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr11:66386400-66387400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:66386400-66387400	Enhancers	Pancreas	Pancrea
16	chr11:66386400-66391600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:66386600-66387200	Weak transcription	Left Ventricle	heart
18	chr11:66386600-66387200	Active TSS	Stomach Smooth Muscle	stomach
19	chr11:66386600-66387400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:66386600-66387400	Weak transcription	Fetal Lung	lung
21	chr11:66386600-66387600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr11:66386600-66387600	Enhancers	Fetal Brain Male	brain
23	chr11:66386600-66388400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:66386600-66388400	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr11:66386600-66388400	Enhancers	Brain Anterior Caudate	brain
26	chr11:66386600-66388400	Weak transcription	Ovary	ovary
27	chr11:66386600-66388600	Weak transcription	Gastric	stomach
28	chr11:66386600-66388800	Genic enhancers	Fetal Muscle Leg	muscle
29	chr11:66386600-66388800	Strong transcription	HSMM	muscle
30	chr11:66386600-66390200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr11:66386600-66390200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr11:66386600-66391600	Enhancers	Stomach Mucosa	stomach
33	chr11:66386800-66387200	Active TSS	Primary T cells fromperipheralblood	blood
34	chr11:66386800-66387200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr11:66386800-66387200	Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr11:66386800-66387200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr11:66386800-66387200	Weak transcription	Colon Smooth Muscle	Colon
38	chr11:66386800-66387200	Active TSS	Duodenum Mucosa	Duodenum
39	chr11:66386800-66387400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr11:66386800-66387400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:66386800-66387400	Active TSS	Primary T cells from cord blood	blood
42	chr11:66386800-66387400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:66386800-66387400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr11:66386800-66387400	Enhancers	Adipose Nuclei	Adipose
45	chr11:66386800-66387400	Active TSS	Brain Angular Gyrus	brain
46	chr11:66386800-66387400	Weak transcription	Brain Substantia Nigra	brain
47	chr11:66386800-66387400	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr11:66386800-66387400	Weak transcription	Fetal Intestine Large	intestine
49	chr11:66386800-66387400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr11:66386800-66387400	Weak transcription	Spleen	Spleen

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