Variant report

Variant	rs544021
Chromosome Location	chr11:66315661-66315662
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:66315520-66315670	Caco-2	colon:	n/a	chr11:66315546-66315559
2	CTCF	chr11:66315520-66315670	WERI-Rb-1	eye:	n/a	chr11:66315546-66315559

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:66313928..66316895-chr11:66444565..66446585,2	K562	blood:
2	chr11:66312120..66315858-chr11:66382093..66385516,4	K562	blood:
3	chr11:66311475..66316022-chr11:66335981..66338223,4	MCF-7	breast:
4	chr11:66246144..66249538-chr11:66312277..66316497,5	MCF-7	breast:
5	chr11:66276681..66279418-chr11:66315413..66317207,2	MCF-7	breast:
6	chr11:66315618..66318263-chr11:66344654..66346591,2	K562	blood:
7	chr11:66311617..66317579-chr11:66325496..66333927,8	MCF-7	breast:
8	chr11:66313372..66315858-chr11:66382227..66384523,2	K562	blood:

No data

Variant related genes	Relation type
ZDHHC24	TF binding region
ENSG00000174483	Chromatin interaction
ENSG00000173914	Chromatin interaction
ENSG00000250105	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000255517	Chromatin interaction
ENSG00000199325	Chromatin interaction
ENSG00000174080	Chromatin interaction
ENSG00000248643	Chromatin interaction
ENSG00000254986	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1791679	0.83[AFR][1000 genomes]
rs1791690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1945302	0.83[AFR][1000 genomes]
rs2511217	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2511224	0.92[YRI][hapmap]
rs490998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs597626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs610293	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs679228	0.84[ASN][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	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	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
4	nsv897787	chr11:66300348-66347850	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs544021	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs544021	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs544021	ACTN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66312800-66316000	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr11:66314000-66315800	Weak transcription	HSMMtube	muscle
3	chr11:66314200-66316600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:66314200-66321400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:66314400-66316200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:66314400-66316400	Weak transcription	Lung	lung
7	chr11:66314400-66320400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:66314400-66327000	Weak transcription	Right Atrium	heart
9	chr11:66314600-66316200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr11:66314600-66317000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr11:66314800-66315800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr11:66314800-66316000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:66314800-66316800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:66314800-66326600	Weak transcription	Psoas Muscle	Psoas
15	chr11:66315000-66316800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr11:66315200-66317000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr11:66315400-66316200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr11:66315400-66316200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:66315400-66316200	Enhancers	HepG2	liver
20	chr11:66315400-66316400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr11:66315400-66316800	Flanking Active TSS	Fetal Muscle Trunk	muscle
22	chr11:66315400-66323600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr11:66315600-66316000	Enhancers	Fetal Muscle Leg	muscle
24	chr11:66315600-66316000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr11:66315600-66316200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr11:66315600-66316200	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr11:66315600-66316200	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr11:66315600-66316600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr11:66315600-66316600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:66315600-66316800	Enhancers	H1 Cell Line	embryonic stem cell
31	chr11:66315600-66316800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr11:66315600-66316800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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