Variant report

Variant	rs12634371
Chromosome Location	chr3:100211325-100211326
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	POLR2A	chr3:100211114-100211550	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:100210863-100211656	HEK293	kidney:	n/a	n/a
3	TAF1	chr3:100210803-100211504	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr3:100211278-100211617	GM12878	blood:	n/a	n/a
5	RFX5	chr3:100211207-100211499	HepG2	liver:	n/a	chr3:100211366-100211375
6	NFYA	chr3:100211180-100211933	GM12878	blood:	n/a	chr3:100211396-100211406 chr3:100211394-100211412 chr3:100211363-100211378 chr3:100211363-100211377 chr3:100211362-100211374 chr3:100211363-100211381 chr3:100211363-100211378
7	POLR2A	chr3:100211137-100211357	A549	lung:	n/a	n/a
8	TBP	chr3:100211109-100211597	K562	blood:	n/a	chr3:100211163-100211174
9	YY1	chr3:100211226-100211501	GM12878	blood:	n/a	chr3:100211247-100211258 chr3:100211418-100211432 chr3:100211245-100211259 chr3:100211425-100211436 chr3:100211419-100211433 chr3:100211242-100211256 chr3:100211355-100211369
10	USF2	chr3:100211239-100211406	HepG2	liver:	n/a	n/a
11	SP2	chr3:100211052-100211674	H1-hESC	embryonic stem cell:	n/a	chr3:100211349-100211372 chr3:100211366-100211376
12	MAX	chr3:100211212-100211679	A549	lung:	n/a	chr3:100211520-100211529
13	POLR2A	chr3:100210600-100211815	H1-hESC	embryonic stem cell:	n/a	n/a
14	YY1	chr3:100211137-100211379	A549	lung:	n/a	chr3:100211247-100211258 chr3:100211245-100211259 chr3:100211242-100211256 chr3:100211355-100211369
15	NFIC	chr3:100211128-100211605	ECC-1	luminal epithelium:	n/a	n/a
16	USF2	chr3:100211093-100211499	H1-hESC	embryonic stem cell:	n/a	chr3:100211420-100211436
17	POLR2A	chr3:100210641-100211845	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr3:100210775-100211951	HepG2	liver:	n/a	n/a
19	RAD21	chr3:100211074-100211550	MCF-7	breast:	n/a	chr3:100211418-100211432
20	PBX3	chr3:100210759-100211738	SK-N-SH	brain:	n/a	chr3:100211366-100211375 chr3:100211351-100211371 chr3:100210771-100210782
21	PBX3	chr3:100211091-100211647	A549	lung:	n/a	chr3:100211366-100211375 chr3:100211351-100211371
22	CREB1	chr3:100211050-100211783	GM12878	blood:	n/a	n/a
23	YY1	chr3:100210816-100211497	SK-N-SH_RA	brain:	n/a	chr3:100211247-100211258 chr3:100211418-100211432 chr3:100211245-100211259 chr3:100211425-100211436 chr3:100211419-100211433 chr3:100211242-100211256 chr3:100211355-100211369
24	SP1	chr3:100211079-100211657	HepG2	liver:	n/a	chr3:100211328-100211337 chr3:100211326-100211338 chr3:100211326-100211338 chr3:100211364-100211385
25	RFX5	chr3:100211260-100211592	GM12878	blood:	n/a	chr3:100211366-100211375
26	NRF1	chr3:100211112-100211392	H1-hESC	embryonic stem cell:	n/a	n/a
27	BRCA1	chr3:100211266-100211401	HepG2	liver:	n/a	n/a
28	HEY1	chr3:100210906-100211580	HepG2	liver:	n/a	chr3:100211422-100211437
29	POLR2A	chr3:100210936-100211692	GM19193	blood:	n/a	n/a
30	BACH1	chr3:100210875-100211675	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr3:100211300-100211450	GM12878	blood:	n/a	n/a
32	SP1	chr3:100210774-100211580	H1-hESC	embryonic stem cell:	n/a	chr3:100211328-100211337 chr3:100211326-100211338 chr3:100211326-100211338 chr3:100211364-100211385 chr3:100211016-100211026
33	USF1	chr3:100211229-100211487	SK-N-SH_RA	brain:	n/a	chr3:100211420-100211436
34	MAX	chr3:100210937-100211793	K562	blood:	n/a	chr3:100211520-100211529
35	E2F6	chr3:100210687-100211716	H1-hESC	embryonic stem cell:	n/a	chr3:100211365-100211374 chr3:100210711-100210718
36	POLR2A	chr3:100210966-100211588	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr3:100211180-100211330	BE2_C	brain:	n/a	n/a
38	MAFK	chr3:100211075-100211439	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr3:100210827-100211557	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr3:100211099-100211333	H1-hESC	embryonic stem cell:	n/a	n/a
41	SIN3AK20	chr3:100210864-100211607	SK-N-SH	brain:	n/a	n/a
42	FOXA1	chr3:100211021-100211680	HepG2	liver:	n/a	n/a
43	RCOR1	chr3:100210907-100211874	Hela-S3	cervix:	n/a	n/a
44	FOS	chr3:100211183-100211583	GM12878	blood:	n/a	n/a
45	POLR2A	chr3:100211178-100211551	MCF-7	breast:	n/a	n/a
46	MAFK	chr3:100211134-100211339	HepG2	liver:	n/a	n/a
47	POLR2A	chr3:100211075-100211673	GM15510	blood:	n/a	n/a
48	POLR2A	chr3:100210926-100211833	GM18951	blood:	n/a	n/a
49	NFYB	chr3:100210702-100211955	GM12878	blood:	n/a	chr3:100211396-100211406 chr3:100211363-100211378 chr3:100211360-100211375 chr3:100211363-100211377 chr3:100211391-100211406 chr3:100211362-100211374 chr3:100211363-100211378
50	TBP	chr3:100210935-100211634	HepG2	liver:	n/a	chr3:100211163-100211174

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:100211280-100211330	HepG2	liver:	n/a
2	chr3:100211280-100211330	GM06990	blood:	n/a
3	chr3:100211280-100211330	ProgFib	skin:	n/a
4	chr3:100211280-100211330	GM12892	blood:	n/a
5	chr3:100211280-100211330	HL-60	blood:	n/a
6	chr3:100211280-100211330	Hepatocyte	liver:	n/a
7	chr3:100211280-100211330	U87	brain:	n/a
8	chr3:100211280-100211330	ovcar-3	ovarian:	n/a
9	chr3:100211280-100211330	MCF-7	breast:	n/a
10	chr3:100211280-100211330	NT2-D1	testis:	n/a
11	chr3:100211280-100211330	HIPEpiC	eye:	n/a
12	chr3:100211280-100211330	T-47D	breast:	n/a
13	chr3:100211280-100211330	HRE	kidney:	n/a
14	chr3:100211280-100211330	CMK	blood:	n/a
15	chr3:100211280-100211330	GM12891	blood:	n/a
16	chr3:100211280-100211330	SK-N-MC	brain:	n/a
17	chr3:100211280-100211330	LNCaP	prostate:	n/a
18	chr3:100211280-100211330	HPAEpiC	pulmonary alveolar:	n/a
19	chr3:100211280-100211330	BJ	skin:	n/a
20	chr3:100211280-100211330	HCT-116	colon:	n/a
21	chr3:100211280-100211330	IMR90	lung:	fetal
22	chr3:100211280-100211330	AG04449	skin:	fetal
23	chr3:100211280-100211330	HCM	heart:	n/a
24	chr3:100211280-100211330	AoSMC	blood vessel:	n/a
25	chr3:100211280-100211330	NHBE	bronchial:	n/a
26	chr3:100211280-100211330	BE2_C	brain:	n/a
27	chr3:100211280-100211330	GM19239	blood:	n/a
28	chr3:100211280-100211330	SAEC	small airway:	n/a
29	chr3:100211280-100211330	AG09319	gingival:	n/a
30	chr3:100211280-100211330	Hela-S3	cervix:	n/a
31	chr3:100211280-100211330	HNPCEpiC	eye:	n/a
32	chr3:100211280-100211330	SKMC	muscle:	n/a
33	chr3:100211280-100211330	SK-N-SH_RA	brain:	n/a
34	chr3:100211280-100211330	HCPEpiC	choroid plexus:	n/a
35	chr3:100211280-100211330	PFSK-1	brain:	n/a
36	chr3:100211280-100211330	AG09309	skin:	n/a
37	chr3:100211280-100211330	Caco-2	colon:	n/a
38	chr3:100211280-100211330	K562	blood:	n/a
39	chr3:100211280-100211330	NB4	blood:	n/a
40	chr3:100211280-100211330	AG04450	lung:	fetal
41	chr3:100211280-100211330	PrEC	prostate:	n/a
42	chr3:100211280-100211330	NHDF-neo	bronchial:	n/a
43	chr3:100211280-100211330	AG10803	skin:	n/a
44	chr3:100211280-100211330	GM12878	blood:	n/a
45	chr3:100211280-100211330	H1-hESC	embryonic stem cell:	embryo
46	chr3:100211280-100211330	A549	lung:	n/a
47	chr3:100211280-100211330	HEEpiC	esophagus:	n/a
48	chr3:100211280-100211330	HUVEC	blood vessel:	n/a
49	chr3:100211280-100211330	RPTEC	kidney:	n/a
50	chr3:100211280-100211330	HCF	heart:	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:1618873..1619547-chr3:100210982..100211748,2	Hela-S3	cervix:
2	chr22:38301815..38302566-chr3:100211020..100211628,2	Hela-S3	cervix:
3	chr12:48147196..48147737-chr3:100210846..100211663,2	Hela-S3	cervix:

Variant related genes	Relation type
TMEM45A	TF binding region
TMEM45A	CpG island
ENSG00000100139	Chromatin interaction
ENSG00000186594	Chromatin interaction
ENSG00000211584	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11923942	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11927516	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12631075	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12636805	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12639465	0.85[EUR][1000 genomes]
rs4928097	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57018910	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59299896	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60071944	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60272820	0.90[EUR][1000 genomes]
rs61636409	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62276517	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62276520	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62276521	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62276522	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62276523	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62276526	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62276556	0.91[EUR][1000 genomes]
rs62276559	0.85[EUR][1000 genomes]
rs66791174	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67600559	0.91[EUR][1000 genomes]
rs6763079	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6763178	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67774605	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6798264	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73152126	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7429072	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7429277	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7429604	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7430698	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7430715	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7431846	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7616839	0.84[ASN][1000 genomes]
rs7640470	0.93[ASN][1000 genomes]
rs9851429	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877218	chr3:100176360-100267619	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12634371	TMEM45A	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100210400-100212200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr3:100210400-100212200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:100210400-100212600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:100210400-100212600	Active TSS	Brain Anterior Caudate	brain
5	chr3:100210600-100211800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:100210600-100211800	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr3:100210600-100212000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr3:100210600-100212000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:100210600-100212000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:100210600-100212000	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr3:100210600-100212000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:100210600-100212000	Active TSS	Brain Substantia Nigra	brain
13	chr3:100210600-100212000	Active TSS	Fetal Heart	heart
14	chr3:100210600-100212000	Active TSS	Pancreas	Pancrea
15	chr3:100210600-100212000	Active TSS	Right Ventricle	heart
16	chr3:100210600-100212200	Active TSS	Brain Germinal Matrix	brain
17	chr3:100210600-100212200	Active TSS	Brain Hippocampus Middle	brain
18	chr3:100210600-100212200	Active TSS	Fetal Muscle Trunk	muscle
19	chr3:100210600-100212200	Active TSS	A549	lung
20	chr3:100210600-100212400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:100210600-100212400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:100210600-100212400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:100210600-100212400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:100210600-100212400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr3:100210600-100212400	Active TSS	Rectal Smooth Muscle	rectum
26	chr3:100210600-100212400	Active TSS	Right Atrium	heart
27	chr3:100210600-100212400	Active TSS	Stomach Smooth Muscle	stomach
28	chr3:100210600-100212800	Active TSS	HSMM	muscle
29	chr3:100210800-100211600	Active TSS	Primary T cells from cord blood	blood
30	chr3:100210800-100211600	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr3:100210800-100211800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:100210800-100211800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:100210800-100211800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:100210800-100211800	Active TSS	Left Ventricle	heart
35	chr3:100210800-100211800	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr3:100210800-100211800	Active TSS	Stomach Mucosa	stomach
37	chr3:100210800-100212000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr3:100210800-100212000	Active TSS	H1 Cell Line	embryonic stem cell
39	chr3:100210800-100212000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:100210800-100212000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:100210800-100212000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:100210800-100212000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
43	chr3:100210800-100212000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:100210800-100212000	Active TSS	Colon Smooth Muscle	Colon
45	chr3:100210800-100212000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr3:100210800-100212000	Active TSS	Fetal Thymus	thymus
47	chr3:100210800-100212000	Active TSS	Psoas Muscle	Psoas
48	chr3:100210800-100212000	Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr3:100210800-100212000	Bivalent/Poised TSS	Thymus	Thymus
50	chr3:100210800-100212200	Active TSS	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links