Variant report

Variant	rs11675908
Chromosome Location	chr2:114588784-114588785
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	CEBPB	chr2:114588630-114588856	A549	lung:	n/a	n/a
2	YY1	chr2:114588730-114589014	K562	blood:	n/a	chr2:114588808-114588820
3	MAFK	chr2:114588627-114589171	K562	blood:	n/a	chr2:114588976-114588991
4	MAX	chr2:114588550-114589155	ECC-1	luminal epithelium:	n/a	n/a
5	JUND	chr2:114588753-114588998	H1-hESC	embryonic stem cell:	n/a	n/a
6	E2F6	chr2:114588698-114589172	A549	lung:	n/a	n/a
7	YY1	chr2:114588658-114588977	H1-hESC	embryonic stem cell:	n/a	chr2:114588808-114588820
8	FOXA1	chr2:114588656-114588977	T-47D	breast:	n/a	n/a
9	FOXA1	chr2:114588657-114588909	T-47D	breast:	n/a	n/a
10	MAX	chr2:114588659-114589207	A549	lung:	n/a	n/a
11	MAX	chr2:114588575-114589297	A549	lung:	n/a	n/a
12	NR3C1	chr2:114588756-114589223	A549	lung:	n/a	n/a
13	MAX	chr2:114588580-114589165	ECC-1	luminal epithelium:	n/a	n/a
14	MAX	chr2:114588763-114588987	H1-hESC	embryonic stem cell:	n/a	n/a
15	GATA3	chr2:114588667-114589030	T-47D	breast:	n/a	n/a
16	MAFF	chr2:114588770-114589183	K562	blood:	n/a	chr2:114588974-114588992
17	YY1	chr2:114588576-114589270	SK-N-SH	brain:	n/a	chr2:114588808-114588820
18	EP300	chr2:114588624-114589026	T-47D	breast:	n/a	n/a
19	YY1	chr2:114588666-114589074	H1-hESC	embryonic stem cell:	n/a	chr2:114588808-114588820
20	JUND	chr2:114588759-114589140	K562	blood:	n/a	n/a
21	YY1	chr2:114588692-114588989	A549	lung:	n/a	chr2:114588808-114588820
22	FOSL2	chr2:114588726-114589218	A549	lung:	n/a	n/a
23	YY1	chr2:114588656-114589088	ECC-1	luminal epithelium:	n/a	chr2:114588808-114588820
24	YY1	chr2:114588634-114589037	ECC-1	luminal epithelium:	n/a	chr2:114588808-114588820

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC35F5-3	chr2:114588626-114589005	ENSG00000228857
2	lnc-SLC35F5-3	chr2:114588429-114589005	NONHSAT073841
3	lnc-SLC35F5-3	chr2:114588760-114589005	NR_110174

Variant related genes	Relation type
ENSG00000244063	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10185135	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10209659	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1028245	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123214	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11676646	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11684182	0.84[ASN][1000 genomes]
rs11685296	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685654	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11691664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403401	0.82[ASN][1000 genomes]
rs17197632	0.81[ASN][1000 genomes]
rs35167892	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4241126	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4292100	0.88[AFR][1000 genomes]
rs4411702	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4571059	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849285	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849286	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849287	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849289	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4849290	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4849291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849294	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57106417	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61050591	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62170141	0.85[AFR][1000 genomes]
rs62170143	0.85[AFR][1000 genomes]
rs62170146	0.82[AFR][1000 genomes]
rs62170148	0.85[AFR][1000 genomes]
rs62170155	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62170159	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62171760	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62171761	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62171768	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62171769	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6542180	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72835407	0.85[AFR][1000 genomes]
rs72835479	0.81[ASN][1000 genomes]
rs72948684	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7576537	0.81[ASN][1000 genomes]
rs7579001	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9646927	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11675908	DDX11L2	cis	Heart Left Ventricle	GTEx
rs11675908	DDX11L2	cis	Adipose Subcutaneous	GTEx
rs11675908	RPL23AP7	cis	Artery Tibial	GTEx
rs11675908	DDX11L2	cis	Whole Blood	GTEx
rs11675908	SLC35F5	cis	Thyroid	GTEx
rs11675908	RPL23AP7	cis	Artery Aorta	GTEx
rs11675908	RPL23AP7	cis	Whole Blood	GTEx
rs11675908	ACTR3	Cis_1M	lymphoblastoid	RTeQTL
rs11675908	DDX11L2	cis	lung	GTEx
rs11675908	DDX11L2	cis	Esophagus Mucosa	GTEx
rs11675908	RPL23AP7	cis	Heart Left Ventricle	GTEx
rs11675908	DDX11L2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114574200-114603600	Weak transcription	Primary B cells from cord blood	blood
2	chr2:114584600-114595600	Weak transcription	HepG2	liver
3	chr2:114584800-114592000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:114585800-114588800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:114586400-114591400	Weak transcription	Fetal Intestine Large	intestine
6	chr2:114586400-114601000	Weak transcription	Primary T cells from cord blood	blood
7	chr2:114587600-114589000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:114587800-114590800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:114588400-114588800	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr2:114588400-114588800	Enhancers	A549	lung
11	chr2:114588400-114589200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr2:114588400-114589200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr2:114588400-114589200	Enhancers	Esophagus	oesophagus
14	chr2:114588400-114589200	Enhancers	NHEK	skin
15	chr2:114588600-114589200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:114588600-114589200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr2:114588600-114589200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:114588600-114589200	Weak transcription	Placenta	Placenta
19	chr2:114588600-114589200	Enhancers	Placenta Amnion	Placenta Amnion
20	chr2:114588600-114589200	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr2:114588600-114589200	Enhancers	HMEC	breast
22	chr2:114588600-114589200	Enhancers	K562	blood

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