Variant report

Variant	rs28398043
Chromosome Location	chr8:40014225-40014226
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	MAFK	chr8:40012542-40014874	Hela-S3	cervix:	n/a	chr8:40012912-40012923
2	MAX	chr8:40012886-40015404	A549	lung:	n/a	chr8:40014429-40014440
3	FOSL2	chr8:40012715-40015353	A549	lung:	n/a	chr8:40013464-40013473 chr8:40014910-40014919
4	EP300	chr8:40013165-40015070	A549	lung:	n/a	chr8:40013624-40013638 chr8:40013984-40013998 chr8:40013466-40013475
5	TCF7L2	chr8:40013712-40014497	HEK293	kidney:	n/a	n/a
6	POLR2A	chr8:40014078-40014238	HepG2	liver:	n/a	n/a
7	POLR2A	chr8:40014172-40014282	A549	lung:	n/a	n/a
8	SMC3	chr8:40012792-40014485	HepG2	liver:	n/a	n/a
9	CHD2	chr8:40012873-40014407	Hela-S3	cervix:	n/a	n/a
10	JUND	chr8:40013096-40014420	A549	lung:	n/a	chr8:40013464-40013473
11	MYBL2	chr8:40010303-40014343	HepG2	liver:	n/a	n/a
12	MAZ	chr8:40013829-40014358	HepG2	liver:	n/a	n/a
13	ZBTB33	chr8:40013509-40014436	A549	lung:	n/a	n/a
14	CHD2	chr8:40014130-40014436	HepG2	liver:	n/a	n/a
15	REST	chr8:40010334-40015499	A549	lung:	n/a	n/a
16	POLR2A	chr8:40010569-40015492	HUVEC	blood vessel:	n/a	n/a
17	SIN3AK20	chr8:40013285-40015056	A549	lung:	n/a	n/a
18	ZBTB33	chr8:40012770-40014832	A549	lung:	n/a	n/a
19	MAX	chr8:40012593-40014343	Hela-S3	cervix:	n/a	n/a
20	TCF12	chr8:40012443-40015515	A549	lung:	n/a	n/a
21	EP300	chr8:40013594-40014922	A549	lung:	n/a	chr8:40013624-40013638 chr8:40013984-40013998
22	ELK4	chr8:40013984-40014374	Hela-S3	cervix:	n/a	n/a
23	BRCA1	chr8:40012317-40014436	Hela-S3	cervix:	n/a	n/a
24	SIX5	chr8:40012519-40015241	A549	lung:	n/a	chr8:40015035-40015051 chr8:40015035-40015051 chr8:40015035-40015051 chr8:40015035-40015051 chr8:40015035-40015051
25	TBP	chr8:40010549-40014322	Hela-S3	cervix:	n/a	n/a
26	FOXA2	chr8:40013613-40014336	A549	lung:	n/a	chr8:40013892-40013904
27	PBX3	chr8:40013812-40014784	A549	lung:	n/a	n/a
28	RAD21	chr8:40012890-40014454	Hela-S3	cervix:	n/a	n/a
29	GATA3	chr8:40013711-40014473	A549	lung:	n/a	chr8:40014389-40014400
30	SIN3AK20	chr8:40013621-40014905	A549	lung:	n/a	n/a
31	RCOR1	chr8:40014071-40014271	HepG2	liver:	n/a	n/a
32	POLR2A	chr8:40010692-40014925	IMR90	lung:	n/a	n/a
33	POLR2A	chr8:40014108-40014292	A549	lung:	n/a	n/a
34	BCL3	chr8:40010543-40015442	A549	lung:	n/a	chr8:40013335-40013344
35	POLR2A	chr8:40012818-40014633	HUVEC	blood vessel:	n/a	n/a
36	PBX3	chr8:40013002-40015129	A549	lung:	n/a	n/a
37	POLR2A	chr8:40010719-40015314	Hela-S3	cervix:	n/a	n/a
38	PRDM1	chr8:40012907-40014521	Hela-S3	cervix:	n/a	chr8:40013408-40013421 chr8:40014052-40014067
39	RFX5	chr8:40012598-40014402	Hela-S3	cervix:	n/a	chr8:40013121-40013134
40	POLR2A	chr8:40012612-40015349	HepG2	liver:	n/a	n/a
41	ELF1	chr8:40013097-40014506	A549	lung:	n/a	n/a
42	TCF12	chr8:40013625-40014417	A549	lung:	n/a	n/a
43	SMC3	chr8:40012659-40014375	Hela-S3	cervix:	n/a	n/a
44	ARID3A	chr8:40012958-40014737	HepG2	liver:	n/a	n/a
45	POLR2A	chr8:40012516-40014338	HepG2	liver:	n/a	n/a
46	POLR2A	chr8:40014114-40014379	A549	lung:	n/a	n/a
47	POLR2A	chr8:40013931-40015141	SK-N-SH	brain:	n/a	n/a
48	NFIC	chr8:40010345-40014340	HepG2	liver:	n/a	n/a
49	STAT3	chr8:40013300-40014363	Hela-S3	cervix:	n/a	chr8:40013989-40014000 chr8:40013333-40013344
50	EP300	chr8:40013292-40014412	Hela-S3	cervix:	n/a	chr8:40013624-40013638 chr8:40013984-40013998 chr8:40013466-40013475

No.	Distal block	Cell Line	Cell type
1	chr8:40012859..40015075-chr8:40035582..40037157,2	MCF-7	breast:
2	chr8:40014106..40017606-chr8:40052102..40057551,6	MCF-7	breast:
3	chr8:40012507..40014336-chr8:40053503..40056480,2	MCF-7	breast:
4	chr8:40013123..40015871-chr8:40028440..40032117,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254143	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10103059	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11780250	0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12541392	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12546288	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12548579	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687838	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4398898	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6983906	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv539555	chr8:39683857-40673606	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv534582	chr8:39884590-40653224	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:40009600-40014600	Active TSS	Rectal Smooth Muscle	rectum
2	chr8:40009600-40014800	Active TSS	Colon Smooth Muscle	Colon
3	chr8:40010200-40014800	Active TSS	Right Atrium	heart
4	chr8:40010200-40015000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr8:40010400-40014400	Active TSS	Ovary	ovary
6	chr8:40010400-40014600	Active TSS	Adipose Nuclei	Adipose
7	chr8:40010800-40016400	Weak transcription	Stomach Mucosa	stomach
8	chr8:40011200-40016200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr8:40011200-40022600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr8:40011400-40014400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr8:40011400-40020000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:40011600-40014800	Weak transcription	Spleen	Spleen
13	chr8:40011600-40016400	Weak transcription	HSMM	muscle
14	chr8:40011800-40014400	Weak transcription	Small Intestine	intestine
15	chr8:40011800-40014800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr8:40011800-40014800	Weak transcription	Pancreas	Pancrea
17	chr8:40011800-40015000	Weak transcription	Lung	lung
18	chr8:40012600-40014800	Transcr. at gene 5' and 3'	A549	lung
19	chr8:40013600-40014600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr8:40013600-40014600	Enhancers	Fetal Intestine Small	intestine
21	chr8:40013600-40014600	Weak transcription	Left Ventricle	heart
22	chr8:40013600-40015000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr8:40013600-40016400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr8:40013600-40016400	Weak transcription	NH-A	brain
25	chr8:40013600-40031600	Weak transcription	Right Ventricle	heart
26	chr8:40013800-40014400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr8:40013800-40015000	Enhancers	Fetal Intestine Large	intestine
28	chr8:40013800-40015400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr8:40013800-40016400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr8:40013800-40019600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr8:40013800-40020200	Enhancers	HepG2	liver
32	chr8:40014000-40014400	Enhancers	Fetal Kidney	kidney
33	chr8:40014000-40014400	Flanking Active TSS	Fetal Lung	lung
34	chr8:40014000-40014400	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr8:40014000-40014800	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr8:40014000-40015000	Weak transcription	Fetal Brain Male	brain
37	chr8:40014000-40015400	Enhancers	Stomach Smooth Muscle	stomach
38	chr8:40014000-40015600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr8:40014000-40017600	Enhancers	HUVEC	blood vessel
40	chr8:40014200-40014400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr8:40014200-40014400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr8:40014200-40014400	Flanking Active TSS	Hela-S3	cervix
43	chr8:40014200-40014600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr8:40014200-40014800	Enhancers	NHDF-Ad	bronchial
45	chr8:40014200-40016200	Weak transcription	NHLF	lung

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