Variant report

Variant	rs62262084
Chromosome Location	chr3:47653822-47653823
allele	C/T
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	chr3:47653669-47654023	U87	brain:	n/a	n/a
2	GATA3	chr3:47653477-47653975	T-47D	breast:	n/a	chr3:47653827-47653834 chr3:47653823-47653839 chr3:47653827-47653834 chr3:47653823-47653839 chr3:47653827-47653834 chr3:47653826-47653836 chr3:47653825-47653837 chr3:47653827-47653836
3	GATA3	chr3:47653551-47654115	SK-N-SH	brain:	n/a	chr3:47653827-47653834 chr3:47653823-47653839 chr3:47653827-47653834 chr3:47653823-47653839 chr3:47653827-47653834 chr3:47653826-47653836 chr3:47653825-47653837 chr3:47653827-47653836
4	NFIC	chr3:47653502-47654146	SK-N-SH	brain:	n/a	chr3:47653865-47653881
5	CEBPB	chr3:47653796-47653995	K562	blood:	n/a	n/a
6	JUND	chr3:47653737-47654036	K562	blood:	n/a	n/a
7	SRF	chr3:47653603-47654199	ECC-1	luminal epithelium:	n/a	chr3:47653918-47653931
8	GATA3	chr3:47653500-47654209	SK-N-SH	brain:	n/a	chr3:47653827-47653834 chr3:47653823-47653839 chr3:47653827-47653834 chr3:47653823-47653839 chr3:47653827-47653834 chr3:47653826-47653836 chr3:47653825-47653837 chr3:47653827-47653836
9	CEBPB	chr3:47653645-47654038	IMR90	lung:	n/a	n/a
10	NFIC	chr3:47653543-47654077	ECC-1	luminal epithelium:	n/a	chr3:47653865-47653881
11	SRF	chr3:47653789-47654203	ECC-1	luminal epithelium:	n/a	chr3:47653918-47653931
12	NFIC	chr3:47653604-47654140	ECC-1	luminal epithelium:	n/a	chr3:47653865-47653881
13	TEAD4	chr3:47653701-47654066	K562	blood:	n/a	n/a
14	CUX1	chr3:47653814-47653923	K562	blood:	n/a	n/a
15	STAT3	chr3:47653348-47653979	MCF10A-Er-Src	breast:	n/a	chr3:47653778-47653786 chr3:47653772-47653786 chr3:47653543-47653551
16	TBL1XR1	chr3:47653721-47653979	K562	blood:	n/a	n/a
17	GATA2	chr3:47653618-47654080	HUVEC	blood vessel:	n/a	chr3:47653827-47653834 chr3:47653823-47653839 chr3:47653827-47653834 chr3:47653823-47653839 chr3:47653827-47653834 chr3:47653826-47653836 chr3:47653825-47653837 chr3:47653827-47653836
18	RCOR1	chr3:47653729-47653955	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47652393..47654345-chr3:47713182..47715815,2	K562	blood:
2	chr3:47652301..47655679-chr3:47656757..47659038,4	K562	blood:
3	chr3:47649126..47651542-chr3:47653050..47654614,2	K562	blood:

Variant related genes	Relation type
SMARCC1	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11707707	0.80[AFR][1000 genomes]
rs11709289	0.86[AMR][1000 genomes]
rs11716779	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11929303	0.83[AFR][1000 genomes]
rs12635438	0.80[AFR][1000 genomes]
rs13085978	0.87[AFR][1000 genomes]
rs17785248	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34448818	0.82[AMR][1000 genomes]
rs35012836	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35664069	0.80[AFR][1000 genomes]
rs5016900	0.82[AMR][1000 genomes]
rs61675361	0.87[AFR][1000 genomes]
rs883662	0.81[AFR][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	esv1835200	chr3:47642233-47654375	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs62262084	MRPS18AP1	cis	Thyroid	GTEx
rs62262084	SMARCC1	Cis_1M	lymphoblastoid	RTeQTL
rs62262084	ZNF589	cis	Nerve Tibial	GTEx
rs62262084	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs62262084	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs62262084	MRPS18AP1	cis	Nerve Tibial	GTEx
rs62262084	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs62262084	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs62262084	MRPS18AP1	cis	Artery Tibial	GTEx
rs62262084	NME6	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47623400-47655000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:47626200-47698600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:47626400-47655600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:47626400-47680600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:47626600-47688600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:47626600-47699800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:47626800-47680800	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr3:47632400-47658600	Weak transcription	A549	lung
9	chr3:47632400-47660800	Weak transcription	Esophagus	oesophagus
10	chr3:47634200-47661000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:47635000-47686800	Strong transcription	Dnd41	blood
12	chr3:47636800-47672800	Weak transcription	Small Intestine	intestine
13	chr3:47637200-47665000	Strong transcription	Primary T cells from cord blood	blood
14	chr3:47638000-47681200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:47638200-47665800	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr3:47639200-47654600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:47639200-47655000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr3:47639200-47655200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:47639200-47655200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:47639200-47655600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:47639200-47675800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr3:47641800-47655800	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:47643600-47684800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:47643800-47666400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:47644000-47654000	Strong transcription	Fetal Thymus	thymus
26	chr3:47644200-47676000	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:47644400-47654200	Strong transcription	Primary B cells from cord blood	blood
28	chr3:47644400-47655200	Strong transcription	GM12878-XiMat	blood
29	chr3:47644400-47664600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr3:47644600-47663800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:47645000-47656600	Strong transcription	K562	blood
32	chr3:47645200-47654200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:47645200-47663200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:47645400-47656800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:47645400-47663600	Strong transcription	HepG2	liver
36	chr3:47645600-47654000	Strong transcription	Liver	Liver
37	chr3:47645800-47664600	Strong transcription	Primary hematopoietic stem cells	blood
38	chr3:47646600-47658600	Strong transcription	Fetal Brain Female	brain
39	chr3:47646600-47666600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:47646800-47654000	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr3:47648000-47670600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:47648400-47654200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
43	chr3:47649200-47654400	Strong transcription	Hela-S3	cervix
44	chr3:47650000-47654600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:47650200-47654200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:47651800-47655000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:47651800-47655200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr3:47651800-47656000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:47651800-47660800	Weak transcription	Gastric	stomach
50	chr3:47651800-47661000	Weak transcription	Colonic Mucosa	Colon

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