Variant report

Variant	rs10406801
Chromosome Location	chr19:41427206-41427207
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:210)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:210 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr19:41426760-41427462	Hela-S3	cervix:	n/a	n/a
2	EP300	chr19:41426868-41427474	K562	blood:	n/a	n/a
3	NR2F2	chr19:41426654-41427763	HepG2	liver:	n/a	n/a
4	RCOR1	chr19:41426865-41427581	K562	blood:	n/a	n/a
5	EP300	chr19:41426628-41427755	T-47D	breast:	n/a	n/a
6	USF1	chr19:41426410-41427720	A549	lung:	n/a	n/a
7	CTCF	chr19:41427140-41427290	SAEC	small airway:	n/a	n/a
8	SP1	chr19:41426158-41428226	A549	lung:	n/a	n/a
9	FOS	chr19:41426848-41427459	HUVEC	blood vessel:	n/a	n/a
10	BHLHE40	chr19:41426976-41427417	HepG2	liver:	n/a	n/a
11	HNF4A	chr19:41426859-41427465	HepG2	liver:	n/a	n/a
12	ZNF263	chr19:41426648-41427680	HEK293-T-REx	kidney:	n/a	n/a
13	EP300	chr19:41427011-41427455	HepG2	liver:	n/a	n/a
14	FOXA2	chr19:41426857-41427726	HepG2	liver:	n/a	n/a
15	JUND	chr19:41426840-41427495	K562	blood:	n/a	chr19:41427099-41427110
16	HNF4A	chr19:41426926-41427277	HepG2	liver:	n/a	n/a
17	FOXM1	chr19:41426885-41427510	MCF-7	breast:	n/a	n/a
18	TFAP2A	chr19:41426702-41427370	Hela-S3	cervix:	n/a	n/a
19	NR3C1	chr19:41426779-41427553	A549	lung:	n/a	n/a
20	FOS	chr19:41426836-41427538	MCF10A-Er-Src	breast:	n/a	n/a
21	MYC	chr19:41426849-41427258	MCF10A-Er-Src	breast:	n/a	n/a
22	RAD21	chr19:41426638-41427819	A549	lung:	n/a	n/a
23	MAFK	chr19:41426806-41427474	K562	blood:	n/a	n/a
24	SP1	chr19:41426694-41427755	HCT-116	colon:	n/a	n/a
25	EP300	chr19:41426058-41428275	A549	lung:	n/a	chr19:41427952-41427966
26	NR2F2	chr19:41426929-41427418	K562	blood:	n/a	n/a
27	KAP1	chr19:41426277-41427784	HEK293	kidney:	n/a	n/a
28	MAX	chr19:41426253-41428040	A549	lung:	n/a	n/a
29	NR3C1	chr19:41426550-41427867	A549	lung:	n/a	n/a
30	MYC	chr19:41427086-41427424	HepG2	liver:	n/a	n/a
31	ATF3	chr19:41426982-41427439	HepG2	liver:	n/a	n/a
32	FOSL2	chr19:41426870-41427383	MCF-7	breast:	n/a	chr19:41427100-41427111
33	ESR1	chr19:41426771-41427717	ECC-1	luminal epithelium:	n/a	n/a
34	ESR1	chr19:41426454-41427805	T-47D	breast:	n/a	n/a
35	REST	chr19:41426567-41427854	A549	lung:	n/a	n/a
36	ESR1	chr19:41426427-41427907	T-47D	breast:	n/a	n/a
37	ETS1	chr19:41426627-41427814	A549	lung:	n/a	n/a
38	ZBTB33	chr19:41426638-41427811	A549	lung:	n/a	n/a
39	GATA3	chr19:41426485-41427991	A549	lung:	n/a	n/a
40	PBX3	chr19:41426691-41427640	A549	lung:	n/a	n/a
41	GATA3	chr19:41426639-41427843	MCF-7	breast:	n/a	n/a
42	MAX	chr19:41426974-41427425	HepG2	liver:	n/a	n/a
43	BCL3	chr19:41426209-41428048	A549	lung:	n/a	n/a
44	STAT3	chr19:41426803-41427242	MCF10A-Er-Src	breast:	n/a	n/a
45	JUND	chr19:41426696-41427515	Hela-S3	cervix:	n/a	chr19:41427099-41427110
46	SIN3AK20	chr19:41426324-41428111	A549	lung:	n/a	n/a
47	TCF12	chr19:41426535-41427890	A549	lung:	n/a	n/a
48	JUND	chr19:41426623-41427677	HCT-116	colon:	n/a	chr19:41427099-41427110
49	EP300	chr19:41426826-41427784	MCF-7	breast:	n/a	n/a
50	SIX5	chr19:41426003-41428376	A549	lung:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41220910..41226186-chr19:41426409..41429163,5	MCF-7	breast:
2	chr19:41426562..41427465-chr19:41557958..41558773,3	MCF-7	breast:
3	chr19:40971826..40972553-chr19:41426973..41427731,2	MCF-7	breast:
4	chr19:41403893..41404465-chr19:41426940..41427721,3	MCF-7	breast:
5	chr19:41403631..41404535-chr19:41426743..41427640,3	MCF-7	breast:

No data

Variant related genes	Relation type
CYP2B7P	TF binding region
ENSG00000123815	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000160460	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11668711	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671237	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3892666	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4001940	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4001941	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4802097	0.80[AMR][1000 genomes]
rs4803403	0.89[ASN][1000 genomes]
rs4803406	0.87[EUR][1000 genomes]
rs7252501	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257201	0.89[ASN][1000 genomes]
rs73555393	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10406801	DHX34	cis	cerebellum	SCAN
rs10406801	PRKD2	cis	parietal	SCAN
rs10406801	PSG4	cis	cerebellum	SCAN
rs10406801	RPS19	cis	parietal	SCAN
rs10406801	ZNF541	cis	parietal	SCAN
rs10406801	ETHE1	cis	parietal	SCAN
rs10406801	PSG9	cis	cerebellum	SCAN
rs10406801	TMEM143	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41426200-41427600	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr19:41426200-41429800	Enhancers	Stomach Mucosa	stomach
3	chr19:41426400-41427600	Weak transcription	Colonic Mucosa	Colon
4	chr19:41426400-41427800	Enhancers	HepG2	liver
5	chr19:41426400-41428000	Enhancers	Hela-S3	cervix
6	chr19:41426400-41429600	Enhancers	Ovary	ovary
7	chr19:41426400-41430200	Enhancers	Fetal Intestine Large	intestine
8	chr19:41426400-41430200	Enhancers	Fetal Intestine Small	intestine
9	chr19:41426600-41427400	Enhancers	HUVEC	blood vessel
10	chr19:41426600-41428200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr19:41426600-41429000	Enhancers	K562	blood
12	chr19:41426600-41429600	Enhancers	Liver	Liver
13	chr19:41426800-41427400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:41426800-41427400	Enhancers	A549	lung
15	chr19:41426800-41427600	Enhancers	Gastric	stomach
16	chr19:41426800-41427600	Enhancers	Pancreas	Pancrea
17	chr19:41427000-41427600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr19:41427000-41428000	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr19:41427000-41429200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:41427200-41427600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr19:41427200-41428000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr19:41427200-41428400	Enhancers	Placenta	Placenta

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