Variant report

Variant	rs2304575
Chromosome Location	chr3:53926110-53926111
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:426)
CpG islands
(count:122)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:426 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:53925592-53926340	HepG2	liver:	n/a	n/a
2	CTCF	chr3:53925892-53926159	Spleen_OC	spleen:	n/a	n/a
3	GABPA	chr3:53925663-53926426	MCF-7	breast:	n/a	n/a
4	POU2F2	chr3:53925373-53926356	GM12878	blood:	n/a	n/a
5	BCLAF1	chr3:53925490-53926439	GM12878	blood:	n/a	chr3:53925670-53925683 chr3:53925669-53925682
6	POLR2A	chr3:53925664-53926255	GM12891	blood:	n/a	n/a
7	GABPA	chr3:53925688-53926253	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:53925563-53926613	U87	brain:	n/a	n/a
9	POLR2A	chr3:53925691-53926147	HepG2	liver:	n/a	n/a
10	MAX	chr3:53925506-53926572	A549	lung:	n/a	n/a
11	SRF	chr3:53925475-53926530	HCT-116	colon:	n/a	n/a
12	NFYB	chr3:53925685-53926353	GM12878	blood:	n/a	chr3:53925950-53925964 chr3:53925949-53925964 chr3:53925951-53925966 chr3:53925952-53925962 chr3:53925949-53925964
13	USF1	chr3:53925865-53926197	A549	lung:	n/a	n/a
14	TAF1	chr3:53925106-53926405	H1-hESC	embryonic stem cell:	n/a	n/a
15	FOS	chr3:53925875-53926390	MCF10A-Er-Src	breast:	n/a	n/a
16	GABPA	chr3:53925792-53926252	HepG2	liver:	n/a	n/a
17	PBX3	chr3:53925674-53926453	SK-N-SH	brain:	n/a	chr3:53925952-53925961
18	YY1	chr3:53925565-53926337	H1-hESC	embryonic stem cell:	n/a	chr3:53925673-53925682 chr3:53926023-53926032
19	MAZ	chr3:53925528-53926396	Hela-S3	cervix:	n/a	n/a
20	SRF	chr3:53925861-53926160	K562	blood:	n/a	n/a
21	POLR2A	chr3:53925214-53926549	Hela-S3	cervix:	n/a	n/a
22	IRF1	chr3:53925655-53926324	K562	blood:	n/a	chr3:53925953-53925962
23	E2F6	chr3:53925457-53926636	K562	blood:	n/a	n/a
24	SRF	chr3:53925842-53926234	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:53925215-53926443	GM19099	blood:	n/a	n/a
26	POLR2A	chr3:53925577-53926385	PANC-1	pancreas:	n/a	n/a
27	YY1	chr3:53925538-53926429	SK-N-SH	brain:	n/a	chr3:53925673-53925682 chr3:53926023-53926032
28	POLR2A	chr3:53925993-53926366	HUVEC	blood vessel:	n/a	n/a
29	TAF1	chr3:53925942-53926270	HepG2	liver:	n/a	n/a
30	PML	chr3:53925445-53926480	GM12878	blood:	n/a	n/a
31	ATF3	chr3:53925838-53926140	K562	blood:	n/a	n/a
32	PBX3	chr3:53925772-53926205	GM12878	blood:	n/a	chr3:53925952-53925961
33	NFIC	chr3:53925562-53926228	HepG2	liver:	n/a	chr3:53925628-53925656
34	CREB1	chr3:53924970-53926510	K562	blood:	n/a	n/a
35	POLR2A	chr3:53925577-53926400	PANC-1	pancreas:	n/a	n/a
36	MAFF	chr3:53925693-53926320	HepG2	liver:	n/a	chr3:53925918-53925936
37	CREB1	chr3:53924997-53926439	GM12878	blood:	n/a	n/a
38	EP300	chr3:53925759-53926312	K562	blood:	n/a	n/a
39	CREB1	chr3:53925732-53926284	A549	lung:	n/a	n/a
40	E2F4	chr3:53925799-53926180	GM12878	blood:	n/a	n/a
41	BCLAF1	chr3:53925463-53926403	GM12878	blood:	n/a	chr3:53925670-53925683 chr3:53925669-53925682
42	SETDB1	chr3:53925733-53926441	U2OS	brain:	n/a	n/a
43	HA-E2F1	chr3:53925654-53926354	MCF-7	breast:	n/a	n/a
44	POLR2A	chr3:53925489-53926467	Gliobla	brain:	n/a	n/a
45	POLR2A	chr3:53925633-53926372	SK-N-MC	brain:	n/a	n/a
46	POLR2A	chr3:53923739-53926749	PBDE	blood:	n/a	n/a
47	YY1	chr3:53925450-53926339	HepG2	liver:	n/a	chr3:53925673-53925682 chr3:53926023-53926032
48	TCF12	chr3:53925689-53926438	ECC-1	luminal epithelium:	n/a	n/a
49	YY1	chr3:53925686-53926316	SK-N-SH_RA	brain:	n/a	chr3:53926023-53926032
50	POLR2A	chr3:53925590-53926409	MCF-7	breast:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:53926080-53926130	HMEC	breast:	n/a
2	chr3:53926080-53926130	Jurkat	blood:	n/a
3	chr3:53926080-53926130	GM06990	blood:	n/a
4	chr3:53926080-53926130	AG10803	skin:	n/a
5	chr3:53926080-53926130	A549	lung:	n/a
6	chr3:53926101-53926151	AG04450	lung:	fetal
7	chr3:53926080-53926130	Hepatocyte	liver:	n/a
8	chr3:53926101-53926151	HCM	heart:	n/a
9	chr3:53926101-53926151	SK-N-MC	brain:	n/a
10	chr3:53926080-53926130	HCPEpiC	choroid plexus:	n/a
11	chr3:53926101-53926151	SKMC	muscle:	n/a
12	chr3:53926101-53926151	AG09319	gingival:	n/a
13	chr3:53926101-53926151	HCF	heart:	n/a
14	chr3:53926080-53926130	GM12891	blood:	n/a
15	chr3:53926101-53926151	SK-N-SH	brain:	n/a
16	chr3:53926080-53926130	PFSK-1	brain:	n/a
17	chr3:53926101-53926151	PANC-1	pancreas:	n/a
18	chr3:53926080-53926130	HAEpiC	amniotic membrane:	n/a
19	chr3:53926101-53926151	HEEpiC	esophagus:	n/a
20	chr3:53926101-53926151	SAEC	small airway:	n/a
21	chr3:53926101-53926151	GM12878	blood:	n/a
22	chr3:53926080-53926130	RPTEC	kidney:	n/a
23	chr3:53926101-53926151	HIPEpiC	eye:	n/a
24	chr3:53926080-53926130	HCT-116	colon:	n/a
25	chr3:53926101-53926151	HRE	kidney:	n/a
26	chr3:53926080-53926130	LNCaP	prostate:	n/a
27	chr3:53926101-53926151	RPTEC	kidney:	n/a
28	chr3:53926080-53926130	NT2-D1	testis:	n/a
29	chr3:53926101-53926151	ProgFib	skin:	n/a
30	chr3:53926080-53926130	NHBE	bronchial:	n/a
31	chr3:53926080-53926130	NHDF-neo	bronchial:	n/a
32	chr3:53926080-53926130	PANC-1	pancreas:	n/a
33	chr3:53926101-53926151	NB4	blood:	n/a
34	chr3:53926101-53926151	NT2-D1	testis:	n/a
35	chr3:53926101-53926151	AG09309	skin:	n/a
36	chr3:53926101-53926151	PFSK-1	brain:	n/a
37	chr3:53926101-53926151	GM19239	blood:	n/a
38	chr3:53926080-53926130	SK-N-SH	brain:	n/a
39	chr3:53926101-53926151	HL-60	blood:	n/a
40	chr3:53926080-53926130	CMK	blood:	n/a
41	chr3:53926101-53926151	Caco-2	colon:	n/a
42	chr3:53926080-53926130	HNPCEpiC	eye:	n/a
43	chr3:53926101-53926151	HCT-116	colon:	n/a
44	chr3:53926080-53926130	HCF	heart:	n/a
45	chr3:53926101-53926151	Jurkat	blood:	n/a
46	chr3:53926080-53926130	GM12878	blood:	n/a
47	chr3:53926101-53926151	U87	brain:	n/a
48	chr3:53926101-53926151	GM06990	blood:	n/a
49	chr3:53926080-53926130	Caco-2	colon:	n/a
50	chr3:53926101-53926151	GM12892	blood:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:53914775..53921125-chr3:53923203..53927129,12	MCF-7	breast:
2	chr12:13043989..13044920-chr3:53925634..53926622,2	Hela-S3	cervix:
3	chr3:53925577..53926163-chr6:56819278..56819811,2	Hela-S3	cervix:
4	chr3:53915297..53916473-chr3:53925441..53926286,3	MCF-7	breast:
5	chr15:72410138..72410841-chr3:53925749..53926410,2	Hela-S3	cervix:
6	chr3:53909521..53911477-chr3:53924349..53927028,2	MCF-7	breast:
7	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
8	chr3:53913820..53918433-chr3:53924406..53927799,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000113811	TF binding region
ENSG00000113811	CpG island
ENSG00000151917	Chromatin interaction
ENSG00000222888	Chromatin interaction
ENSG00000066933	Chromatin interaction
ENSG00000166192	Chromatin interaction
ENSG00000013588	Chromatin interaction
ENSG00000151914	Chromatin interaction
ENSG00000113812	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1020082	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1134091	0.88[EUR][1000 genomes]
rs12632292	0.96[EUR][1000 genomes]
rs17053568	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17053590	0.90[EUR][1000 genomes]
rs1982171	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241806	0.96[EUR][1000 genomes]
rs2276840	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276843	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276844	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276845	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289203	0.89[EUR][1000 genomes]
rs2304576	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2884631	0.84[EUR][1000 genomes]
rs3017	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3733075	0.83[EUR][1000 genomes]
rs3733079	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3733083	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3821868	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3821869	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41292476	0.86[EUR][1000 genomes]
rs4141606	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs45511795	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687594	0.96[EUR][1000 genomes]
rs4687753	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4687756	0.90[EUR][1000 genomes]
rs4687758	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687760	0.85[EUR][1000 genomes]
rs55917919	0.91[EUR][1000 genomes]
rs56743403	0.89[EUR][1000 genomes]
rs57398949	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62253003	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62253004	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6445612	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs709324	0.84[EUR][1000 genomes]
rs73078007	0.84[EUR][1000 genomes]
rs9840445	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9849951	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9850063	0.96[EUR][1000 genomes]
rs9860367	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9880056	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs999515	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv876804	chr3:53833509-53934171	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1010575	chr3:53846741-53934781	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv997771	chr3:53852695-53926635	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1002141	chr3:53858541-53934781	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv1014752	chr3:53912429-54123246	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2304575	ACTR8	cis	Thyroid	GTEx
rs2304575	SELK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53923400-53926400	Active TSS	Right Ventricle	heart
2	chr3:53923600-53926600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr3:53924000-53926400	Active TSS	Colonic Mucosa	Colon
4	chr3:53924200-53926600	Active TSS	Psoas Muscle	Psoas
5	chr3:53924200-53926600	Active TSS	Right Atrium	heart
6	chr3:53924200-53926800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:53924400-53926400	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr3:53924400-53926400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:53924400-53926800	Active TSS	HSMMtube	muscle
10	chr3:53924600-53926400	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr3:53924600-53926400	Active TSS	Fetal Intestine Large	intestine
12	chr3:53924600-53926400	Active TSS	GM12878-XiMat	blood
13	chr3:53924600-53926600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr3:53924600-53926800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr3:53924600-53926800	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:53924600-53926800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:53924800-53926200	Active TSS	HMEC	breast
18	chr3:53924800-53926400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:53924800-53926400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:53924800-53926400	Active TSS	Aorta	Aorta
21	chr3:53924800-53926400	Active TSS	Lung	lung
22	chr3:53924800-53926400	Active TSS	Pancreas	Pancrea
23	chr3:53924800-53926600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr3:53924800-53926600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:53924800-53926600	Active TSS	Esophagus	oesophagus
26	chr3:53924800-53926600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr3:53924800-53926800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:53924800-53926800	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr3:53924800-53926800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:53924800-53926800	Active TSS	Fetal Muscle Trunk	muscle
31	chr3:53924800-53927000	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr3:53925000-53926200	Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr3:53925000-53926200	Bivalent/Poised TSS	HepG2	liver
34	chr3:53925000-53926200	Active TSS	NH-A	brain
35	chr3:53925000-53926200	Active TSS	NHEK	skin
36	chr3:53925000-53926400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:53925000-53926400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:53925000-53926400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:53925000-53926400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:53925000-53926400	Active TSS	Fetal Intestine Small	intestine
41	chr3:53925000-53926400	Active TSS	Ovary	ovary
42	chr3:53925000-53926400	Active TSS	Small Intestine	intestine
43	chr3:53925000-53926400	Active TSS	NHDF-Ad	bronchial
44	chr3:53925000-53926600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:53925000-53926600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:53925000-53926600	Active TSS	Placenta Amnion	Placenta Amnion
47	chr3:53925000-53926600	Active TSS	HSMM	muscle
48	chr3:53925000-53926600	Active TSS	K562	blood
49	chr3:53925000-53926800	Active TSS	H9 Cell Line	embryonic stem cell
50	chr3:53925000-53926800	Active TSS	Brain Hippocampus Middle	brain

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