Variant report

Variant	rs4001941
Chromosome Location	chr19:41426424-41426425
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	USF1	chr19:41426410-41427720	A549	lung:	n/a	n/a
2	SP1	chr19:41426158-41428226	A549	lung:	n/a	n/a
3	EP300	chr19:41426058-41428275	A549	lung:	n/a	chr19:41427952-41427966
4	KAP1	chr19:41426277-41427784	HEK293	kidney:	n/a	n/a
5	MAX	chr19:41426253-41428040	A549	lung:	n/a	n/a
6	BCL3	chr19:41426209-41428048	A549	lung:	n/a	n/a
7	SIN3AK20	chr19:41426324-41428111	A549	lung:	n/a	n/a
8	SIX5	chr19:41426003-41428376	A549	lung:	n/a	n/a
9	ESR1	chr19:41426343-41427897	T-47D	breast:	n/a	n/a
10	ETS1	chr19:41426380-41428011	A549	lung:	n/a	n/a
11	KAP1	chr19:41426380-41427950	U2OS	brain:	n/a	n/a
12	EP300	chr19:41426278-41428262	A549	lung:	n/a	chr19:41427952-41427966
13	ATF3	chr19:41426280-41428001	A549	lung:	n/a	n/a
14	MAX	chr19:41426167-41428156	A549	lung:	n/a	n/a
15	ESR1	chr19:41426376-41427929	T-47D	breast:	n/a	n/a
16	SP1	chr19:41426223-41428603	A549	lung:	n/a	n/a
17	BCL3	chr19:41426105-41428005	A549	lung:	n/a	n/a
18	ESR1	chr19:41426411-41427864	T-47D	breast:	n/a	n/a
19	TEAD4	chr19:41426254-41427721	A549	lung:	n/a	n/a
20	EP300	chr19:41426395-41427789	T-47D	breast:	n/a	n/a
21	SETDB1	chr19:41425130-41427507	U2OS	brain:	n/a	n/a
22	GATA3	chr19:41426095-41428186	A549	lung:	n/a	n/a
23	FOXA2	chr19:41426314-41427927	A549	lung:	n/a	n/a
24	SIN3AK20	chr19:41426237-41427866	A549	lung:	n/a	n/a
25	CEBPB	chr19:41426226-41428113	A549	lung:	n/a	chr19:41427674-41427685 chr19:41427674-41427685
26	TCF12	chr19:41426009-41428703	A549	lung:	n/a	n/a
27	USF1	chr19:41426202-41428006	A549	lung:	n/a	n/a
28	FOSL2	chr19:41426058-41428179	A549	lung:	n/a	chr19:41427100-41427111
29	REST	chr19:41426064-41428338	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41220910..41226186-chr19:41426409..41429163,5	MCF-7	breast:

Variant related genes	Relation type
CYP2B7P	TF binding region
ENSG00000086544	Chromatin interaction
ENSG00000123815	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10406801	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11668711	0.93[ASN][1000 genomes]
rs11671237	0.91[ASN][1000 genomes]
rs3892666	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4001940	0.82[ASN][1000 genomes]
rs4803403	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252501	0.93[ASN][1000 genomes]
rs7257201	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73555393	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv3337314	chr19:41388910-41534583	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv437830	chr19:41408746-41515702	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv437831	chr19:41416072-41524087	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4001941	FBXO46	cis	cerebellum	SCAN
rs4001941	GPR77	cis	parietal	SCAN
rs4001941	TMEM143	cis	parietal	SCAN
rs4001941	SULT2B1	cis	cerebellum	SCAN
rs4001941	GLTSCR1	cis	cerebellum	SCAN
rs4001941	ETHE1	cis	parietal	SCAN
rs4001941	ZNF541	cis	parietal	SCAN
rs4001941	LOC390940	cis	cerebellum	SCAN
rs4001941	DHX34	cis	cerebellum	SCAN
rs4001941	MYPOP	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41426200-41426600	Flanking Bivalent TSS/Enh	A549	lung
2	chr19:41426200-41427600	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr19:41426200-41429800	Enhancers	Stomach Mucosa	stomach
4	chr19:41426400-41426600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:41426400-41426600	Flanking Active TSS	Liver	Liver
6	chr19:41426400-41427600	Weak transcription	Colonic Mucosa	Colon
7	chr19:41426400-41427800	Enhancers	HepG2	liver
8	chr19:41426400-41428000	Enhancers	Hela-S3	cervix
9	chr19:41426400-41429600	Enhancers	Ovary	ovary
10	chr19:41426400-41430200	Enhancers	Fetal Intestine Large	intestine
11	chr19:41426400-41430200	Enhancers	Fetal Intestine Small	intestine

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