Variant report

Variant	rs6827817
Chromosome Location	chr4:88330987-88330988
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	NR3C1	chr4:88330556-88331082	A549	lung:	n/a	chr4:88330666-88330692 chr4:88330666-88330692 chr4:88330672-88330686 chr4:88330671-88330687 chr4:88330666-88330692 chr4:88330670-88330688 chr4:88330666-88330692 chr4:88330671-88330687 chr4:88330672-88330686 chr4:88330666-88330692
2	FOXA1	chr4:88330465-88331109	HepG2	liver:	n/a	n/a
3	MBD4	chr4:88330525-88331000	HepG2	liver:	n/a	n/a
4	FOXA1	chr4:88330426-88331116	A549	lung:	n/a	n/a
5	TCF7L2	chr4:88330415-88332369	HEK293	kidney:	n/a	n/a
6	SP1	chr4:88330431-88331064	HepG2	liver:	n/a	n/a
7	TEAD4	chr4:88330268-88331081	HepG2	liver:	n/a	n/a
8	TBL1XR1	chr4:88330674-88330993	K562	blood:	n/a	n/a
9	SP1	chr4:88330447-88331238	A549	lung:	n/a	n/a
10	TAL1	chr4:88330623-88330989	K562	blood:	n/a	n/a
11	FOXA2	chr4:88330545-88331125	A549	lung:	n/a	n/a
12	EGR1	chr4:88330940-88331208	K562	blood:	n/a	n/a
13	FOXA1	chr4:88330461-88331102	HepG2	liver:	n/a	n/a
14	FOXA1	chr4:88330484-88331102	HepG2	liver:	n/a	n/a
15	FOXA1	chr4:88330463-88331106	A549	lung:	n/a	n/a
16	GATA3	chr4:88330491-88331037	A549	lung:	n/a	chr4:88330785-88330795 chr4:88330875-88330885 chr4:88330875-88330882
17	TEAD4	chr4:88330611-88331068	K562	blood:	n/a	n/a
18	NR2F2	chr4:88330373-88331224	HepG2	liver:	n/a	n/a
19	NR2F2	chr4:88330448-88331109	HepG2	liver:	n/a	n/a
20	RCOR1	chr4:88330676-88331152	K562	blood:	n/a	n/a
21	HDAC2	chr4:88330519-88331013	HepG2	liver:	n/a	n/a
22	GATA3	chr4:88330539-88331142	A549	lung:	n/a	chr4:88330785-88330795 chr4:88330875-88330885 chr4:88330875-88330882
23	HNF4G	chr4:88330556-88331033	HepG2	liver:	n/a	n/a
24	HDAC2	chr4:88330476-88331136	HepG2	liver:	n/a	n/a
25	MYBL2	chr4:88330475-88331317	HepG2	liver:	n/a	n/a
26	TCF12	chr4:88330348-88331797	A549	lung:	n/a	n/a
27	NR3C1	chr4:88330471-88331046	A549	lung:	n/a	chr4:88330666-88330692 chr4:88330666-88330692 chr4:88330672-88330686 chr4:88330671-88330687 chr4:88330666-88330692 chr4:88330670-88330688 chr4:88330666-88330692 chr4:88330671-88330687 chr4:88330672-88330686 chr4:88330666-88330692
28	FOXA2	chr4:88330491-88331085	HepG2	liver:	n/a	n/a
29	SP1	chr4:88330556-88331015	A549	lung:	n/a	n/a
30	KAP1	chr4:88330302-88332262	HEK293	kidney:	n/a	n/a
31	CEBPD	chr4:88330635-88331109	K562	blood:	n/a	n/a
32	KAP1	chr4:88330287-88332199	U2OS	brain:	n/a	n/a
33	NFIC	chr4:88330534-88331075	HepG2	liver:	n/a	n/a
34	HNF4A	chr4:88330540-88331013	HepG2	liver:	n/a	n/a
35	NR3C1	chr4:88330501-88331001	A549	lung:	n/a	chr4:88330666-88330692 chr4:88330666-88330692 chr4:88330672-88330686 chr4:88330671-88330687 chr4:88330666-88330692 chr4:88330670-88330688 chr4:88330666-88330692 chr4:88330671-88330687 chr4:88330672-88330686 chr4:88330666-88330692
36	RCOR1	chr4:88330814-88330991	K562	blood:	n/a	n/a
37	FOXA2	chr4:88330608-88331151	A549	lung:	n/a	n/a
38	CCNT2	chr4:88330606-88331051	K562	blood:	n/a	n/a
39	EP300	chr4:88330467-88331435	HepG2	liver:	n/a	chr4:88330527-88330541
40	NFIC	chr4:88330438-88331103	HepG2	liver:	n/a	n/a
41	MYBL2	chr4:88330402-88331022	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:88329509..88332282-chr4:88332311..88334966,2	MCF-7	breast:
2	chr4:88330031..88331610-chr4:88342950..88345346,2	K562	blood:
3	chr4:88310329..88313185-chr4:88330457..88332566,2	K562	blood:

Variant related genes	Relation type
ENSG00000249262	TF binding region
ENSG00000251716	TF binding region
ENSG00000198189	Chromatin interaction
ENSG00000251716	Chromatin interaction
ENSG00000170502	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11945232	0.82[GIH][hapmap]
rs28654511	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28713542	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34856449	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6826695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7688038	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7699237	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6827817	EYA1	trans	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88327200-88332400	Enhancers	Fetal Intestine Small	intestine
2	chr4:88327600-88332400	Enhancers	Fetal Intestine Large	intestine
3	chr4:88328000-88331200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:88329000-88331200	Weak transcription	Fetal Lung	lung
5	chr4:88329200-88331000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr4:88329400-88332400	Enhancers	Liver	Liver
7	chr4:88329600-88331000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:88329600-88342600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:88330000-88331000	Enhancers	Duodenum Mucosa	Duodenum
10	chr4:88330000-88331000	Weak transcription	Pancreas	Pancrea
11	chr4:88330000-88331400	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr4:88330000-88331800	Enhancers	Stomach Mucosa	stomach
13	chr4:88330200-88332200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr4:88330200-88332400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:88330400-88331400	Flanking Active TSS	HepG2	liver
16	chr4:88330600-88332000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr4:88330600-88332000	Enhancers	K562	blood
18	chr4:88330800-88331000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:88330800-88332000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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