Variant report

Variant	rs2276846
Chromosome Location	chr3:53916316-53916317
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:274)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:274 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ETS1	chr3:53915921-53916380	A549	lung:	n/a	chr3:53916299-53916310
2	MXI1	chr3:53914153-53917137	SK-N-SH	brain:	n/a	n/a
3	NRF1	chr3:53916024-53916344	K562	blood:	n/a	chr3:53916198-53916209 chr3:53916196-53916210 chr3:53916199-53916208 chr3:53916199-53916210 chr3:53916301-53916310 chr3:53916213-53916224
4	CREB1	chr3:53916033-53916349	A549	lung:	n/a	n/a
5	POLR2A	chr3:53915820-53916402	PFSK-1	brain:	n/a	n/a
6	TAF7	chr3:53915768-53916390	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAZ	chr3:53915631-53916668	K562	blood:	n/a	chr3:53915928-53915938
8	POLR2A	chr3:53915590-53916354	K562	blood:	n/a	n/a
9	TAF1	chr3:53915659-53916417	A549	lung:	n/a	n/a
10	BCLAF1	chr3:53915471-53916369	GM12878	blood:	n/a	chr3:53915953-53915962
11	POLR2A	chr3:53915529-53916476	H1-hESC	embryonic stem cell:	n/a	n/a
12	ELF1	chr3:53915497-53916386	GM12878	blood:	n/a	n/a
13	CEBPD	chr3:53915854-53916376	HepG2	liver:	n/a	n/a
14	TBP	chr3:53915660-53916401	K562	blood:	n/a	n/a
15	PAX5	chr3:53915745-53916354	GM12878	blood:	n/a	n/a
16	YY1	chr3:53915807-53916659	GM12892	blood:	n/a	chr3:53916222-53916242 chr3:53916301-53916310
17	POLR2A	chr3:53915582-53916339	K562	blood:	n/a	n/a
18	IRF1	chr3:53916017-53916565	K562	blood:	n/a	chr3:53916300-53916314
19	MYC	chr3:53915692-53916489	NB4	blood:	n/a	chr3:53915928-53915938
20	REST	chr3:53915771-53916419	H1-neurons	neurons:	n/a	chr3:53915821-53915834
21	TAF1	chr3:53915630-53916376	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr3:53915634-53916528	HUVEC	blood vessel:	n/a	n/a
23	ELF1	chr3:53915646-53916346	K562	blood:	n/a	n/a
24	YY1	chr3:53915315-53916620	SK-N-SH	brain:	n/a	chr3:53916222-53916242 chr3:53916301-53916310
25	POLR2A	chr3:53915613-53916332	A549	lung:	n/a	n/a
26	TAF1	chr3:53915906-53916354	PFSK-1	brain:	n/a	n/a
27	TBL1XR1	chr3:53915650-53916400	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:53915551-53916460	GM12878	blood:	n/a	n/a
29	MAX	chr3:53915587-53916412	ECC-1	luminal epithelium:	n/a	chr3:53915928-53915938
30	POLR2A	chr3:53915772-53916589	HepG2	liver:	n/a	n/a
31	POLR2A	chr3:53915666-53918109	HepG2	liver:	n/a	n/a
32	POLR2A	chr3:53915879-53916459	HepG2	liver:	n/a	n/a
33	GTF2F1	chr3:53915908-53916557	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr3:53915579-53916566	Hela-S3	cervix:	n/a	n/a
35	RCOR1	chr3:53915665-53916385	K562	blood:	n/a	n/a
36	RUNX3	chr3:53915482-53916459	GM12878	blood:	n/a	n/a
37	TCF12	chr3:53915700-53916357	GM12878	blood:	n/a	chr3:53915819-53915826
38	POLR2A	chr3:53915591-53916455	MCF-7	breast:	n/a	n/a
39	TAF1	chr3:53915838-53916347	GM12892	blood:	n/a	n/a
40	REST	chr3:53915837-53916348	HepG2	liver:	n/a	n/a
41	POLR2A	chr3:53915606-53916431	HEK293	kidney:	n/a	n/a
42	POLR2A	chr3:53915584-53916449	HL-60	blood:	n/a	n/a
43	YY1	chr3:53915503-53916558	GM12878	blood:	n/a	chr3:53916222-53916242 chr3:53916301-53916310
44	MAZ	chr3:53915007-53917351	IMR90	lung:	n/a	chr3:53915928-53915938
45	REST	chr3:53915761-53916336	A549	lung:	n/a	chr3:53915821-53915834
46	RUNX3	chr3:53915515-53916434	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:53915480-53916411	GM12892	blood:	n/a	n/a
48	SIX5	chr3:53916036-53916386	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:53915616-53916346	GM10847	blood:	n/a	n/a
50	GABPA	chr3:53915503-53916419	MCF-7	breast:	n/a	chr3:53916196-53916210 chr3:53916199-53916208 chr3:53916199-53916210 chr3:53916301-53916310

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:53916291-53916341	BJ	skin:	n/a
2	chr3:53916291-53916341	NB4	blood:	n/a
3	chr3:53916291-53916341	HRPEpiC	eye:	n/a
4	chr3:53916291-53916341	HPAEpiC	pulmonary alveolar:	n/a
5	chr3:53916291-53916341	NT2-D1	testis:	n/a
6	chr3:53916291-53916341	HCPEpiC	choroid plexus:	n/a
7	chr3:53916291-53916341	GM06990	blood:	n/a
8	chr3:53916291-53916341	A549	lung:	n/a
9	chr3:53916291-53916341	HRCEpiC	kidney:	n/a
10	chr3:53916291-53916341	PANC-1	pancreas:	n/a
11	chr3:53916291-53916341	HIPEpiC	eye:	n/a
12	chr3:53916291-53916341	Hela-S3	cervix:	n/a
13	chr3:53916291-53916341	NHBE	bronchial:	n/a
14	chr3:53916291-53916341	NHDF-neo	bronchial:	n/a
15	chr3:53916291-53916341	MCF10A-Er-Src	breast:	n/a
16	chr3:53916291-53916341	HMEC	breast:	n/a
17	chr3:53916291-53916341	RPTEC	kidney:	n/a
18	chr3:53916291-53916341	HEK293	kidney:	embryo
19	chr3:53916291-53916341	AoSMC	blood vessel:	n/a
20	chr3:53916291-53916341	HCT-116	colon:	n/a
21	chr3:53916291-53916341	HUVEC	blood vessel:	n/a
22	chr3:53916291-53916341	LNCaP	prostate:	n/a
23	chr3:53916291-53916341	U87	brain:	n/a
24	chr3:53916291-53916341	ECC-1	luminal epithelium:	n/a
25	chr3:53916291-53916341	Caco-2	colon:	n/a
26	chr3:53916291-53916341	SK-N-MC	brain:	n/a
27	chr3:53916291-53916341	H1-hESC	embryonic stem cell:	embryo
28	chr3:53916291-53916341	AG04449	skin:	fetal
29	chr3:53916291-53916341	HEEpiC	esophagus:	n/a
30	chr3:53916291-53916341	CMK	blood:	n/a
31	chr3:53916291-53916341	HRE	kidney:	n/a
32	chr3:53916291-53916341	K562	blood:	n/a
33	chr3:53916291-53916341	SK-N-SH	brain:	n/a
34	chr3:53916291-53916341	HCF	heart:	n/a
35	chr3:53916291-53916341	GM19239	blood:	n/a
36	chr3:53916291-53916341	HAEpiC	amniotic membrane:	n/a
37	chr3:53916291-53916341	AG09309	skin:	n/a
38	chr3:53916291-53916341	PFSK-1	brain:	n/a
39	chr3:53916291-53916341	PrEC	prostate:	n/a
40	chr3:53916291-53916341	GM12878	blood:	n/a
41	chr3:53916291-53916341	AG09319	gingival:	n/a
42	chr3:53916291-53916341	HCM	heart:	n/a
43	chr3:53916291-53916341	ProgFib	skin:	n/a
44	chr3:53916291-53916341	ovcar-3	ovarian:	n/a
45	chr3:53916291-53916341	AG04450	lung:	fetal
46	chr3:53916291-53916341	SKMC	muscle:	n/a
47	chr3:53916291-53916341	SAEC	small airway:	n/a
48	chr3:53916291-53916341	Jurkat	blood:	n/a
49	chr3:53916291-53916341	T-47D	breast:	n/a
50	chr3:53916291-53916341	Hepatocyte	liver:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr3:53908420..53912131-chr3:53913956..53917012,3	MCF-7	breast:
2	chr3:53913333..53919757-chr3:53920203..53928086,26	K562	blood:
3	chr3:53914775..53921125-chr3:53923203..53927129,12	MCF-7	breast:
4	chr11:76571922..76572822-chr3:53915731..53916676,2	Hela-S3	cervix:
5	chr3:53915297..53916473-chr3:53925441..53926286,3	MCF-7	breast:
6	chr3:53913820..53918433-chr3:53924406..53927799,6	MCF-7	breast:
7	chr3:53901391..53905529-chr3:53913413..53917026,5	MCF-7	breast:
8	chr3:53880225..53881825-chr3:53914407..53917091,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000222888	TF binding region
ACTR8	TF binding region
ENSG00000222888	CpG island
ACTR8	CpG island
ENSG00000016391	Chromatin interaction
ENSG00000113812	Chromatin interaction
ENSG00000056736	Chromatin interaction
ENSG00000078124	Chromatin interaction
ENSG00000113811	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10440151	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1046677	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1134092	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1157175	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072145	1.00[ASN][1000 genomes]
rs13315972	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1982172	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1992155	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083127	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733073	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3733081	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816144	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821867	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4569647	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687757	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687763	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624599	0.93[ASN][1000 genomes]
rs7636856	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893367	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311516	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311518	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822471	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840079	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840362	0.93[ASN][1000 genomes]
rs9869505	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878207	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878562	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs999514	0.97[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2276846	SELK	Cis_1M	lymphoblastoid	RTeQTL
rs2276846	RP11-884K10.7	cis	Muscle Skeletal	GTEx
rs2276846	IL17RB	cis	Artery Tibial	GTEx
rs2276846	ACTR8	cis	Muscle Skeletal	GTEx
rs2276846	IL17RB	cis	Whole Blood	GTEx
rs2276846	ACTR8	cis	lung	GTEx
rs2276846	ACTR8	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53914800-53916600	Active TSS	Fetal Muscle Trunk	muscle
2	chr3:53915000-53916800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr3:53915200-53916400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:53915200-53916400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:53915200-53916400	Active TSS	Psoas Muscle	Psoas
6	chr3:53915200-53916600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr3:53915200-53916600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:53915200-53916600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:53915200-53916600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:53915200-53916600	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr3:53915200-53916600	Active TSS	Aorta	Aorta
12	chr3:53915200-53916600	Active TSS	Fetal Intestine Small	intestine
13	chr3:53915200-53916600	Active TSS	Left Ventricle	heart
14	chr3:53915200-53916600	Active TSS	Lung	lung
15	chr3:53915200-53916600	Active TSS	Pancreas	Pancrea
16	chr3:53915200-53916600	Active TSS	A549	lung
17	chr3:53915200-53916600	Active TSS	NHDF-Ad	bronchial
18	chr3:53915200-53916600	Active TSS	NHLF	lung
19	chr3:53915200-53916800	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr3:53915200-53916800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:53915200-53916800	Active TSS	Fetal Brain Male	brain
22	chr3:53915200-53916800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr3:53915400-53916400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:53915400-53916400	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr3:53915400-53916400	Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr3:53915400-53916400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:53915400-53916400	Active TSS	Brain Cingulate Gyrus	brain
28	chr3:53915400-53916400	Active TSS	Brain Hippocampus Middle	brain
29	chr3:53915400-53916400	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr3:53915400-53916400	Active TSS	Brain Substantia Nigra	brain
31	chr3:53915400-53916400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr3:53915400-53916400	Active TSS	Fetal Heart	heart
33	chr3:53915400-53916400	Active TSS	Fetal Muscle Leg	muscle
34	chr3:53915400-53916400	Active TSS	Fetal Thymus	thymus
35	chr3:53915400-53916400	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr3:53915400-53916400	Active TSS	Dnd41	blood
37	chr3:53915400-53916400	Active TSS	GM12878-XiMat	blood
38	chr3:53915400-53916400	Active TSS	Hela-S3	cervix
39	chr3:53915400-53916400	Active TSS	HepG2	liver
40	chr3:53915400-53916400	Active TSS	HUVEC	blood vessel
41	chr3:53915400-53916600	Active TSS	H1 Cell Line	embryonic stem cell
42	chr3:53915400-53916600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr3:53915400-53916600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:53915400-53916600	Active TSS	H9 Cell Line	embryonic stem cell
45	chr3:53915400-53916600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:53915400-53916600	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr3:53915400-53916600	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr3:53915400-53916600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:53915400-53916600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:53915400-53916600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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