Variant report

Variant	rs12602852
Chromosome Location	chr17:45054608-45054609
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	JUN	chr17:45053843-45055193	K562	blood:	n/a	chr17:45054210-45054220 chr17:45054211-45054219
2	CBX3	chr17:45054592-45055044	K562	blood:	n/a	n/a
3	NR2F2	chr17:45053840-45055058	K562	blood:	n/a	n/a
4	MAX	chr17:45054592-45055206	A549	lung:	n/a	n/a
5	CTBP2	chr17:45054130-45055406	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr17:45054567-45055644	A549	lung:	n/a	chr17:45054893-45054901
7	RAD21	chr17:45054587-45055119	H1-hESC	embryonic stem cell:	n/a	chr17:45054891-45054905
8	CTCF	chr17:45054560-45054710	HPF	lung:	n/a	n/a
9	YY1	chr17:45054573-45055138	H1-hESC	embryonic stem cell:	n/a	chr17:45054974-45054986
10	CTCF	chr17:45054480-45054630	HVMF	connective:	n/a	n/a
11	KAP1	chr17:45054051-45055096	U2OS	brain:	n/a	chr17:45054767-45054775
12	CTCF	chr17:45054592-45055038	K562	blood:	n/a	chr17:45054893-45054901
13	CTCF	chr17:45054585-45055074	K562	blood:	n/a	chr17:45054893-45054901
14	CTCF	chr17:45054598-45055158	MCF-7	breast:	n/a	chr17:45054893-45054901

Variant related genes	Relation type
LRRC37A17P	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1004485	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079746	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12947916	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3844225	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851788	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213046	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7215119	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7216984	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1067211	chr17:44979111-45057620	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
9	nsv543378	chr17:44979111-45057620	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
10	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12602852	MYL4	cis	lung	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45037400-45055800	Weak transcription	Aorta	Aorta
2	chr17:45040200-45055600	Weak transcription	Pancreas	Pancrea
3	chr17:45046200-45055400	Weak transcription	Spleen	Spleen
4	chr17:45052600-45055200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:45053200-45056000	Weak transcription	HepG2	liver
6	chr17:45053800-45055000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:45054000-45054800	Flanking Active TSS	K562	blood
8	chr17:45054000-45055000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr17:45054200-45054800	Enhancers	A549	lung
10	chr17:45054200-45055200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr17:45054200-45055200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr17:45054200-45055400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:45054200-45055400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
14	chr17:45054200-45055800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
15	chr17:45054200-45055800	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr17:45054200-45056000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr17:45054400-45054800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
18	chr17:45054400-45054800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
19	chr17:45054400-45054800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
20	chr17:45054400-45054800	Bivalent Enhancer	Fetal Brain Female	brain
21	chr17:45054400-45054800	Bivalent Enhancer	Placenta	Placenta
22	chr17:45054400-45055000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr17:45054400-45055000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr17:45054400-45055400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
25	chr17:45054400-45055600	Bivalent Enhancer	Fetal Brain Male	brain
26	chr17:45054400-45055800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr17:45054400-45055800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
28	chr17:45054400-45056000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr17:45054400-45057000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
30	chr17:45054600-45054800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
31	chr17:45054600-45054800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
32	chr17:45054600-45054800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
33	chr17:45054600-45054800	Bivalent Enhancer	Lung	lung
34	chr17:45054600-45055000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr17:45054600-45055200	Bivalent Enhancer	Brain Germinal Matrix	brain
36	chr17:45054600-45055400	Active TSS	H9 Cell Line	embryonic stem cell
37	chr17:45054600-45055800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
38	chr17:45054600-45056400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr17:45054600-45056800	Bivalent Enhancer	Fetal Heart	heart

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