Variant report

Variant	rs1004485
Chromosome Location	chr17:45053997-45053998
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	JUN	chr17:45053843-45055193	K562	blood:	n/a	chr17:45054210-45054220 chr17:45054211-45054219
2	TEAD4	chr17:45053945-45054457	K562	blood:	n/a	n/a
3	CTCF	chr17:45053980-45054130	MCF-7	breast:	n/a	n/a
4	ELF1	chr17:45053979-45054461	K562	blood:	n/a	n/a
5	CEBPB	chr17:45053779-45054263	K562	blood:	n/a	n/a
6	MAZ	chr17:45053988-45054339	K562	blood:	n/a	n/a
7	CTCF	chr17:45053951-45054331	K562	blood:	n/a	n/a
8	REST	chr17:45053979-45054517	K562	blood:	n/a	chr17:45054225-45054234
9	CTCF	chr17:45053947-45054474	K562	blood:	n/a	n/a
10	NR2F2	chr17:45053840-45055058	K562	blood:	n/a	n/a
11	CTCF	chr17:45053866-45054375	MCF-7	breast:	n/a	n/a
12	STAT5A	chr17:45053908-45054447	K562	blood:	n/a	chr17:45054248-45054255
13	CTCF	chr17:45053948-45054372	K562	blood:	n/a	n/a
14	CTCF	chr17:45053977-45054332	H1-hESC	embryonic stem cell:	n/a	n/a
15	CBX3	chr17:45053920-45054565	K562	blood:	n/a	n/a
16	MAX	chr17:45053931-45054580	K562	blood:	n/a	n/a
17	TBL1XR1	chr17:45053991-45054253	K562	blood:	n/a	n/a
18	YY1	chr17:45053987-45054263	K562	blood:	n/a	n/a
19	CTCF	chr17:45053942-45054294	H1-hESC	embryonic stem cell:	n/a	n/a
20	FOSL1	chr17:45053926-45054410	K562	blood:	n/a	chr17:45054210-45054220 chr17:45054211-45054219
21	RAD21	chr17:45053989-45054270	K562	blood:	n/a	n/a
22	JUND	chr17:45053994-45054487	K562	blood:	n/a	chr17:45054210-45054220 chr17:45054211-45054219
23	CTCF	chr17:45053971-45054365	K562	blood:	n/a	n/a
24	ATF3	chr17:45053966-45054375	K562	blood:	n/a	n/a
25	TEAD4	chr17:45053886-45054564	K562	blood:	n/a	n/a
26	RAD21	chr17:45053958-45054296	K562	blood:	n/a	n/a
27	CEBPB	chr17:45053721-45054308	K562	blood:	n/a	n/a
28	CTCF	chr17:45053980-45054130	HVMF	connective:	n/a	n/a
29	TEAD4	chr17:45053958-45054245	H1-hESC	embryonic stem cell:	n/a	n/a
30	ZNF143	chr17:45053989-45054323	K562	blood:	n/a	n/a
31	RAD21	chr17:45053935-45054378	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
LRRC37A17P	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11079746	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12602852	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12947916	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3844225	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851791	0.83[GIH][hapmap]
rs7213046	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7214920	0.83[GIH][hapmap]
rs7215119	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7216984	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1004485	KRT16	cis	cerebellum	SCAN
rs1004485	IGFBP4	cis	parietal	SCAN
rs1004485	GOSR2	cis	cerebellum	SCAN
rs1004485	SKAP1	cis	cerebellum	SCAN
rs1004485	KRT31	cis	parietal	SCAN
rs1004485	MYL4	cis	lung	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45027400-45054000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr17:45036600-45054400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr17:45037400-45055800	Weak transcription	Aorta	Aorta
4	chr17:45040200-45055600	Weak transcription	Pancreas	Pancrea
5	chr17:45043000-45054000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr17:45046200-45055400	Weak transcription	Spleen	Spleen
7	chr17:45046800-45054000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr17:45052600-45055200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr17:45053200-45054000	Enhancers	K562	blood
10	chr17:45053200-45054200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:45053200-45056000	Weak transcription	HepG2	liver
12	chr17:45053400-45054000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr17:45053800-45054200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr17:45053800-45054200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr17:45053800-45055000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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