Variant report

Variant	rs2276845
Chromosome Location	chr3:53916130-53916131
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	SMC3	chr3:53915550-53916266	Hela-S3	cervix:	n/a	n/a
2	ETS1	chr3:53915921-53916380	A549	lung:	n/a	chr3:53916299-53916310
3	MXI1	chr3:53914153-53917137	SK-N-SH	brain:	n/a	n/a
4	MAX	chr3:53915788-53916270	GM12878	blood:	n/a	chr3:53915928-53915938
5	PAX5	chr3:53915625-53916302	GM12878	blood:	n/a	n/a
6	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
7	ZNF143	chr3:53915820-53916256	Hela-S3	cervix:	n/a	n/a
8	CREB1	chr3:53916033-53916349	A549	lung:	n/a	n/a
9	POLR2A	chr3:53915820-53916402	PFSK-1	brain:	n/a	n/a
10	TAF7	chr3:53915768-53916390	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAZ	chr3:53915631-53916668	K562	blood:	n/a	chr3:53915928-53915938
12	POLR2A	chr3:53915590-53916354	K562	blood:	n/a	n/a
13	BHLHE40	chr3:53915760-53916144	K562	blood:	n/a	n/a
14	TAF1	chr3:53915659-53916417	A549	lung:	n/a	n/a
15	BCLAF1	chr3:53915471-53916369	GM12878	blood:	n/a	chr3:53915953-53915962
16	POLR2A	chr3:53915529-53916476	H1-hESC	embryonic stem cell:	n/a	n/a
17	ELF1	chr3:53915497-53916386	GM12878	blood:	n/a	n/a
18	CEBPD	chr3:53915854-53916376	HepG2	liver:	n/a	n/a
19	TBP	chr3:53915660-53916401	K562	blood:	n/a	n/a
20	PAX5	chr3:53915745-53916354	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:53915914-53916244	A549	lung:	n/a	n/a
22	YY1	chr3:53915807-53916659	GM12892	blood:	n/a	chr3:53916222-53916242 chr3:53916301-53916310
23	POLR2A	chr3:53915582-53916339	K562	blood:	n/a	n/a
24	IRF1	chr3:53916017-53916565	K562	blood:	n/a	chr3:53916300-53916314
25	MYC	chr3:53915692-53916489	NB4	blood:	n/a	chr3:53915928-53915938
26	REST	chr3:53915771-53916419	H1-neurons	neurons:	n/a	chr3:53915821-53915834
27	TAF1	chr3:53915630-53916376	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr3:53915634-53916528	HUVEC	blood vessel:	n/a	n/a
29	ZKSCAN1	chr3:53915747-53916283	Hela-S3	cervix:	n/a	n/a
30	ELF1	chr3:53915646-53916346	K562	blood:	n/a	n/a
31	CHD1	chr3:53915930-53916235	H1-hESC	embryonic stem cell:	n/a	chr3:53915933-53915943
32	YY1	chr3:53915315-53916620	SK-N-SH	brain:	n/a	chr3:53916222-53916242 chr3:53916301-53916310
33	MAX	chr3:53915778-53916136	HepG2	liver:	n/a	chr3:53915928-53915938
34	POLR2A	chr3:53915613-53916332	A549	lung:	n/a	n/a
35	TAF1	chr3:53915906-53916354	PFSK-1	brain:	n/a	n/a
36	POLR2A	chr3:53915637-53916261	HepG2	liver:	n/a	n/a
37	TCF12	chr3:53916081-53916288	GM12878	blood:	n/a	n/a
38	TBL1XR1	chr3:53915650-53916400	GM12878	blood:	n/a	n/a
39	CTCF	chr3:53916080-53916230	GM12867	blood:	n/a	n/a
40	POLR2A	chr3:53915551-53916460	GM12878	blood:	n/a	n/a
41	MAX	chr3:53915587-53916412	ECC-1	luminal epithelium:	n/a	chr3:53915928-53915938
42	POLR2A	chr3:53915772-53916589	HepG2	liver:	n/a	n/a
43	POLR2A	chr3:53915666-53918109	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:53915879-53916459	HepG2	liver:	n/a	n/a
45	GTF2F1	chr3:53915908-53916557	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr3:53915579-53916566	Hela-S3	cervix:	n/a	n/a
47	TAF7	chr3:53916079-53916207	K562	blood:	n/a	n/a
48	RCOR1	chr3:53915665-53916385	K562	blood:	n/a	n/a
49	RUNX3	chr3:53915482-53916459	GM12878	blood:	n/a	n/a
50	TCF12	chr3:53915700-53916357	GM12878	blood:	n/a	chr3:53915819-53915826

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	chr15:34516727..34517701-chr3:53915643..53916154,2	Hela-S3	cervix:
4	chr3:53914775..53921125-chr3:53923203..53927129,12	MCF-7	breast:
5	chr11:76571922..76572822-chr3:53915731..53916676,2	Hela-S3	cervix:
6	chr3:53915297..53916473-chr3:53925441..53926286,3	MCF-7	breast:
7	chr3:53913820..53918433-chr3:53924406..53927799,6	MCF-7	breast:
8	chr3:53901391..53905529-chr3:53913413..53917026,5	MCF-7	breast:
9	chr3:53880225..53881825-chr3:53914407..53917091,2	MCF-7	breast:

Variant related genes	Relation type
ACTR8	TF binding region
ENSG00000113811	Chromatin interaction
ENSG00000113812	Chromatin interaction
ENSG00000078124	Chromatin interaction
ENSG00000016391	Chromatin interaction
ENSG00000056736	Chromatin interaction
ENSG00000128463	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1020082	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1134091	0.90[EUR][1000 genomes]
rs12632292	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17053568	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17053590	0.92[EUR][1000 genomes]
rs1982171	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241806	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2276840	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2276843	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276844	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2289203	0.92[EUR][1000 genomes]
rs2304575	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304576	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2884631	0.87[EUR][1000 genomes]
rs3017	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3733075	0.86[EUR][1000 genomes]
rs3733079	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733083	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821868	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821869	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41292476	0.88[EUR][1000 genomes]
rs4141606	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs45511795	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687594	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4687753	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4687756	0.92[EUR][1000 genomes]
rs4687758	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687760	0.87[EUR][1000 genomes]
rs55917919	0.93[EUR][1000 genomes]
rs56743403	0.92[EUR][1000 genomes]
rs57398949	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62253003	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62253004	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6445612	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs709324	0.87[EUR][1000 genomes]
rs73078007	0.84[EUR][1000 genomes]
rs9840445	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9849951	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9850063	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9860367	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9880056	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs999515	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2276845	ACTR8	cis	Thyroid	GTEx
rs2276845	SELK	Cis_1M	lymphoblastoid	RTeQTL
rs2276845	ENSG00000113812	cis	multi-tissue	Pritchard

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	chr3:53915200-53916200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr3:53915200-53916400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:53915200-53916400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:53915200-53916400	Active TSS	Psoas Muscle	Psoas
7	chr3:53915200-53916600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr3:53915200-53916600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:53915200-53916600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:53915200-53916600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:53915200-53916600	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr3:53915200-53916600	Active TSS	Aorta	Aorta
13	chr3:53915200-53916600	Active TSS	Fetal Intestine Small	intestine
14	chr3:53915200-53916600	Active TSS	Left Ventricle	heart
15	chr3:53915200-53916600	Active TSS	Lung	lung
16	chr3:53915200-53916600	Active TSS	Pancreas	Pancrea
17	chr3:53915200-53916600	Active TSS	A549	lung
18	chr3:53915200-53916600	Active TSS	NHDF-Ad	bronchial
19	chr3:53915200-53916600	Active TSS	NHLF	lung
20	chr3:53915200-53916800	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr3:53915200-53916800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:53915200-53916800	Active TSS	Fetal Brain Male	brain
23	chr3:53915200-53916800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr3:53915400-53916200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:53915400-53916200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:53915400-53916400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:53915400-53916400	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr3:53915400-53916400	Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr3:53915400-53916400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:53915400-53916400	Active TSS	Brain Cingulate Gyrus	brain
31	chr3:53915400-53916400	Active TSS	Brain Hippocampus Middle	brain
32	chr3:53915400-53916400	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr3:53915400-53916400	Active TSS	Brain Substantia Nigra	brain
34	chr3:53915400-53916400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr3:53915400-53916400	Active TSS	Fetal Heart	heart
36	chr3:53915400-53916400	Active TSS	Fetal Muscle Leg	muscle
37	chr3:53915400-53916400	Active TSS	Fetal Thymus	thymus
38	chr3:53915400-53916400	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr3:53915400-53916400	Active TSS	Dnd41	blood
40	chr3:53915400-53916400	Active TSS	GM12878-XiMat	blood
41	chr3:53915400-53916400	Active TSS	Hela-S3	cervix
42	chr3:53915400-53916400	Active TSS	HepG2	liver
43	chr3:53915400-53916400	Active TSS	HUVEC	blood vessel
44	chr3:53915400-53916600	Active TSS	H1 Cell Line	embryonic stem cell
45	chr3:53915400-53916600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:53915400-53916600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:53915400-53916600	Active TSS	H9 Cell Line	embryonic stem cell
48	chr3:53915400-53916600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:53915400-53916600	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr3:53915400-53916600	Active TSS	iPS-15b Cell Line	embryonic stem cell

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