Variant report

Variant	rs3851788
Chromosome Location	chr17:45054149-45054150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:104)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:104 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr17:45054046-45054508	K562	blood:	n/a	n/a
2	HDAC2	chr17:45054063-45054336	K562	blood:	n/a	n/a
3	CTCF	chr17:45054100-45054250	NB4	blood:	n/a	n/a
4	JUN	chr17:45053843-45055193	K562	blood:	n/a	chr17:45054210-45054220 chr17:45054211-45054219
5	CTCF	chr17:45054100-45054250	SK-N-SH_RA	brain:	n/a	n/a
6	HDAC2	chr17:45054013-45054475	K562	blood:	n/a	n/a
7	CTCF	chr17:45054060-45054210	HEEpiC	esophagus:	n/a	n/a
8	TAL1	chr17:45054029-45054489	K562	blood:	n/a	n/a
9	TEAD4	chr17:45053945-45054457	K562	blood:	n/a	n/a
10	CTCF	chr17:45054120-45054270	HRE	kidney:	n/a	n/a
11	CTCF	chr17:45054075-45054251	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr17:45054135-45054209	HUVEC	blood vessel:	n/a	n/a
13	ELF1	chr17:45053979-45054461	K562	blood:	n/a	n/a
14	CEBPB	chr17:45053779-45054263	K562	blood:	n/a	n/a
15	BACH1	chr17:45054044-45054344	K562	blood:	n/a	n/a
16	MAZ	chr17:45053988-45054339	K562	blood:	n/a	n/a
17	BHLHE40	chr17:45054062-45054517	K562	blood:	n/a	n/a
18	CTCF	chr17:45054080-45054230	K562	blood:	n/a	n/a
19	CTCF	chr17:45053951-45054331	K562	blood:	n/a	n/a
20	CTCF	chr17:45054106-45054251	MCF-7	breast:	n/a	n/a
21	MYC	chr17:45054062-45054302	K562	blood:	n/a	n/a
22	MAX	chr17:45054030-45054286	K562	blood:	n/a	n/a
23	ARID3A	chr17:45054125-45054359	K562	blood:	n/a	n/a
24	REST	chr17:45053979-45054517	K562	blood:	n/a	chr17:45054225-45054234
25	CTCF	chr17:45053947-45054474	K562	blood:	n/a	n/a
26	CTCF	chr17:45054100-45054250	HepG2	liver:	n/a	n/a
27	RFX5	chr17:45054121-45054321	K562	blood:	n/a	chr17:45054204-45054221
28	CTCF	chr17:45054120-45054270	GM12873	blood:	n/a	n/a
29	NR2F2	chr17:45053840-45055058	K562	blood:	n/a	n/a
30	UBTF	chr17:45054001-45054416	K562	blood:	n/a	n/a
31	CTCF	chr17:45054117-45054250	MCF-7	breast:	n/a	n/a
32	RCOR1	chr17:45054036-45054474	K562	blood:	n/a	n/a
33	ZMIZ1	chr17:45054026-45054478	K562	blood:	n/a	n/a
34	CTCF	chr17:45054125-45054232	MCF-7	breast:	n/a	n/a
35	CTCF	chr17:45054080-45054230	SAEC	small airway:	n/a	n/a
36	CTCF	chr17:45053866-45054375	MCF-7	breast:	n/a	n/a
37	CTCF	chr17:45054080-45054230	GM12873	blood:	n/a	n/a
38	STAT5A	chr17:45053908-45054447	K562	blood:	n/a	chr17:45054248-45054255
39	CTBP2	chr17:45054130-45055406	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr17:45054120-45054270	SK-N-SH_RA	brain:	n/a	n/a
41	CTCF	chr17:45054100-45054250	HPAF	blood vessel:	n/a	n/a
42	CTCF	chr17:45053948-45054372	K562	blood:	n/a	n/a
43	MYC	chr17:45054021-45054403	K562	blood:	n/a	n/a
44	ELK1	chr17:45054130-45054319	K562	blood:	n/a	n/a
45	CTCF	chr17:45054000-45054150	HEEpiC	esophagus:	n/a	n/a
46	POLR2A	chr17:45054065-45054481	K562	blood:	n/a	n/a
47	CTCF	chr17:45053977-45054332	H1-hESC	embryonic stem cell:	n/a	n/a
48	CBX3	chr17:45053920-45054565	K562	blood:	n/a	n/a
49	EP300	chr17:45054042-45054333	K562	blood:	n/a	n/a
50	CTCF	chr17:45054080-45054230	WERI-Rb-1	eye:	n/a	n/a

No data

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]
rs1004485	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]
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]
rs3851791	0.83[GIH][hapmap]
rs7213046	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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
rs3851788	GOSR2	cis	cerebellum	SCAN
rs3851788	KRT31	cis	parietal	SCAN
rs3851788	MYL4	cis	lung	GTEx
rs3851788	SKAP1	cis	cerebellum	SCAN
rs3851788	IGFBP4	cis	parietal	SCAN
rs3851788	KRT16	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45036600-45054400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr17:45037400-45055800	Weak transcription	Aorta	Aorta
3	chr17:45040200-45055600	Weak transcription	Pancreas	Pancrea
4	chr17:45046200-45055400	Weak transcription	Spleen	Spleen
5	chr17:45052600-45055200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr17:45053200-45054200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:45053200-45056000	Weak transcription	HepG2	liver
8	chr17:45053800-45054200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr17:45053800-45054200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr17:45053800-45055000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr17:45054000-45054200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr17:45054000-45054200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
13	chr17:45054000-45054200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
14	chr17:45054000-45054400	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr17:45054000-45054400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
16	chr17:45054000-45054600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr17:45054000-45054600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
18	chr17:45054000-45054600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
19	chr17:45054000-45054800	Flanking Active TSS	K562	blood
20	chr17:45054000-45055000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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