Variant report

Variant	rs1028245
Chromosome Location	chr2:114601335-114601336
allele	G/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	FOS	chr2:114600492-114601462	MCF10A-Er-Src	breast:	n/a	chr2:114600644-114600654 chr2:114600646-114600653 chr2:114600645-114600653 chr2:114600645-114600653 chr2:114600644-114600654 chr2:114600644-114600654 chr2:114600644-114600654
2	STAT3	chr2:114600949-114601401	MCF10A-Er-Src	breast:	n/a	chr2:114601248-114601256
3	GATA3	chr2:114600527-114601523	SK-N-SH	brain:	n/a	chr2:114600825-114600832 chr2:114600643-114600652
4	MYC	chr2:114601047-114601501	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr2:114601032-114601486	ECC-1	luminal epithelium:	n/a	chr2:114601268-114601281
6	CEBPB	chr2:114601070-114601454	IMR90	lung:	n/a	chr2:114601268-114601281
7	POLR2A	chr2:114600874-114601525	MCF10A-Er-Src	breast:	n/a	n/a
8	E2F4	chr2:114601155-114601384	MCF10A-Er-Src	breast:	n/a	n/a
9	GATA3	chr2:114600503-114601428	SK-N-SH	brain:	n/a	chr2:114600825-114600832 chr2:114600643-114600652
10	FOS	chr2:114601056-114601378	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr2:114601073-114601458	ECC-1	luminal epithelium:	n/a	chr2:114601268-114601281
12	STAT3	chr2:114600872-114601492	MCF10A-Er-Src	breast:	n/a	chr2:114601248-114601256
13	MYC	chr2:114601010-114601525	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr2:114601049-114601472	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr2:114600871-114601448	MCF10A-Er-Src	breast:	n/a	chr2:114601248-114601256
16	FOS	chr2:114600527-114601464	MCF10A-Er-Src	breast:	n/a	chr2:114600644-114600654 chr2:114600646-114600653 chr2:114600645-114600653 chr2:114600645-114600653 chr2:114600644-114600654 chr2:114600644-114600654 chr2:114600644-114600654
17	STAT3	chr2:114600892-114601377	MCF10A-Er-Src	breast:	n/a	chr2:114601248-114601256
18	GATA3	chr2:114601013-114601407	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114513011..114515179-chr2:114599381..114601639,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228857	TF binding region
ENSG00000115084	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10185135	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10209659	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11123214	0.91[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11675908	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676646	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11684182	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs11685296	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685654	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11691664	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403401	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17197632	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs35167892	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4241126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4292100	0.80[AFR][1000 genomes]
rs4411702	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4571059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849287	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849289	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4849290	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4849291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849294	0.91[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57106417	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61050591	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62170155	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62170159	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62171760	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62171761	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62171768	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62171769	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6542180	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6642	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs72835479	0.81[ASN][1000 genomes]
rs72948684	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7576537	0.81[ASN][1000 genomes]
rs7579001	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7605071	0.83[CHB][hapmap]
rs9646927	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1028245	RPL23AP7	cis	Heart Left Ventricle	GTEx
rs1028245	CHCHD5	cis	cerebellum	SCAN
rs1028245	DDX11L2	cis	Heart Left Ventricle	GTEx
rs1028245	RPL23AP7	cis	Artery Tibial	GTEx
rs1028245	SLC35F5	cis	Thyroid	GTEx
rs1028245	DDX11L2	cis	Esophagus Mucosa	GTEx
rs1028245	DDX11L2	cis	Esophagus Muscularis	GTEx
rs1028245	RPL23AP7	cis	Artery Aorta	GTEx
rs1028245	RPL23AP7	cis	Whole Blood	GTEx
rs1028245	DDX11L2	cis	Whole Blood	GTEx
rs1028245	ACTR3	Cis_1M	lymphoblastoid	RTeQTL
rs1028245	DDX11L2	cis	lung	GTEx
rs1028245	DDX11L2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:24 , 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	chr2:114596400-114621000	Weak transcription	Aorta	Aorta
3	chr2:114596600-114603400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr2:114596600-114611600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:114596800-114632800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:114597600-114631400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr2:114600000-114601800	Enhancers	Placenta	Placenta
8	chr2:114600000-114602600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:114600200-114601400	Enhancers	K562	blood
10	chr2:114600200-114602000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:114600800-114601400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:114600800-114601400	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr2:114600800-114601600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:114600800-114601600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:114601000-114601400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:114601000-114601400	Strong transcription	Primary T cells from cord blood	blood
17	chr2:114601000-114601400	Active TSS	NHDF-Ad	bronchial
18	chr2:114601000-114601400	Active TSS	NHEK	skin
19	chr2:114601200-114601600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:114601200-114601600	Weak transcription	Osteobl	bone
21	chr2:114601200-114602000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:114601200-114602200	Enhancers	HMEC	breast
23	chr2:114601200-114606200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:114601200-114606800	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links