Variant report

Variant	rs2525507
Chromosome Location	chr14:68938364-68938365
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	EBF1	chr14:68938104-68938533	GM12878	blood:	n/a	n/a
2	MEF2A	chr14:68938155-68938673	GM12878	blood:	n/a	n/a
3	POLR2A	chr14:68938299-68938957	H1-hESC	embryonic stem cell:	n/a	n/a
4	HDAC2	chr14:68938083-68938692	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr14:68937878-68938744	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr14:68937953-68938399	GM12878	blood:	n/a	n/a
7	BATF	chr14:68938127-68938591	GM12878	blood:	n/a	n/a
8	MTA3	chr14:68937957-68938829	GM12878	blood:	n/a	n/a
9	ATF2	chr14:68937895-68938587	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr14:68938035-68938615	H1-hESC	embryonic stem cell:	n/a	chr14:68938450-68938460
11	RAD21	chr14:68938123-68938597	GM12878	blood:	n/a	n/a
12	YY1	chr14:68938335-68938675	GM12878	blood:	n/a	n/a
13	PML	chr14:68937908-68938795	GM12878	blood:	n/a	n/a
14	BATF	chr14:68938187-68938504	GM12878	blood:	n/a	n/a
15	NANOG	chr14:68938053-68938379	H1-hESC	embryonic stem cell:	n/a	chr14:68938175-68938186
16	YY1	chr14:68937851-68938664	H1-hESC	embryonic stem cell:	n/a	n/a
17	STAT5A	chr14:68938170-68938789	GM12878	blood:	n/a	chr14:68938244-68938256 chr14:68938569-68938576
18	RAD21	chr14:68937973-68938737	H1-hESC	embryonic stem cell:	n/a	n/a
19	YY1	chr14:68937794-68938404	H1-hESC	embryonic stem cell:	n/a	n/a
20	JUND	chr14:68938026-68938677	H1-hESC	embryonic stem cell:	n/a	chr14:68938377-68938389
21	SP1	chr14:68937883-68938710	H1-hESC	embryonic stem cell:	n/a	chr14:68938451-68938465
22	SP4	chr14:68937990-68938442	H1-hESC	embryonic stem cell:	n/a	n/a
23	RUNX3	chr14:68938133-68938668	GM12878	blood:	n/a	n/a
24	ATF2	chr14:68938117-68938646	GM12878	blood:	n/a	n/a
25	NFIC	chr14:68938126-68938691	GM12878	blood:	n/a	n/a
26	EP300	chr14:68937976-68938642	H1-hESC	embryonic stem cell:	n/a	n/a
27	MTA3	chr14:68937744-68939084	GM12878	blood:	n/a	n/a
28	SP1	chr14:68937896-68938774	H1-hESC	embryonic stem cell:	n/a	chr14:68938451-68938465
29	CTBP2	chr14:68937638-68939221	H1-hESC	embryonic stem cell:	n/a	n/a
30	RUNX3	chr14:68937971-68938781	GM12878	blood:	n/a	n/a
31	SMC3	chr14:68938274-68938659	GM12878	blood:	n/a	chr14:68938606-68938613
32	STAT1	chr14:68938192-68938366	GM12878	blood:	n/a	chr14:68938244-68938256
33	NFIC	chr14:68938018-68938688	GM12878	blood:	n/a	n/a
34	TBP	chr14:68937964-68938769	H1-hESC	embryonic stem cell:	n/a	n/a
35	RAD21	chr14:68937751-68938824	H1-hESC	embryonic stem cell:	n/a	n/a
36	ZNF384	chr14:68937944-68938870	GM12878	blood:	n/a	n/a
37	WRNIP1	chr14:68938177-68938919	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:68930492..68947840-chr14:69251918..69264148,62	MCF-7	breast:
2	chr14:68924822..68938526-chr14:69257377..69265713,29	MCF-7	breast:
3	chr14:68934455..68938409-chr14:69031168..69034448,4	MCF-7	breast:

Variant related genes	Relation type
RAD51B	TF binding region
ENSG00000185650	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10454686	0.85[CEU][hapmap]
rs11158737	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11158742	1.00[JPT][hapmap]
rs12435006	1.00[JPT][hapmap]
rs12588330	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12889206	1.00[MEX][hapmap]
rs12897307	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17755674	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs1956538	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs2064910	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2331703	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2331704	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2753403	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784118	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs3966077	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4899241	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4899243	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902571	0.90[CEU][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs4902578	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs4902580	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4902581	1.00[JPT][hapmap]
rs4902582	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4902587	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4902588	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4902589	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6573834	1.00[MEX][hapmap]
rs66597987	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7140827	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7145422	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs7150454	1.00[MEX][hapmap]
rs72727487	0.92[ASN][1000 genomes]
rs8003606	1.00[CHB][hapmap]
rs8009876	1.00[MEX][hapmap];1.00[YRI][hapmap]
rs8010430	0.92[ASN][1000 genomes]
rs8013026	0.85[CEU][hapmap]
rs8015516	0.90[CEU][hapmap];0.86[MEX][hapmap]
rs8019592	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9323510	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9323511	0.84[AMR][1000 genomes]
rs9743896	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs975422	0.89[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2525507	NCRNA00238	cis	cerebellum	SCAN
rs2525507	C14orf50	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68926200-68940000	Weak transcription	Ovary	ovary
2	chr14:68927600-68943800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr14:68928400-68939400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr14:68928600-68949000	Weak transcription	Thymus	Thymus
5	chr14:68932200-68950000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr14:68933000-68946600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr14:68933400-68943000	Weak transcription	Right Atrium	heart
8	chr14:68933400-68943400	Weak transcription	Left Ventricle	heart
9	chr14:68933600-68939800	Weak transcription	Fetal Stomach	stomach
10	chr14:68933600-68942800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr14:68933600-68950600	Weak transcription	Aorta	Aorta
12	chr14:68933800-68942600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr14:68934200-68946200	Enhancers	Primary B cells from peripheral blood	blood
14	chr14:68934400-68939800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr14:68934800-68940200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr14:68935000-68940400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr14:68935200-68940200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr14:68935200-68940200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr14:68935400-68938600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr14:68935400-68940200	Enhancers	H1 Cell Line	embryonic stem cell
21	chr14:68935400-68940200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr14:68935400-68940200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr14:68935400-68940800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr14:68935400-68943400	Weak transcription	Fetal Thymus	thymus
25	chr14:68935600-68938600	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr14:68935600-68938600	Weak transcription	Spleen	Spleen
27	chr14:68935600-68940200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr14:68935800-68940800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr14:68935800-68943200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr14:68935800-68943400	Weak transcription	Gastric	stomach
31	chr14:68936000-68938600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr14:68936000-68940000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr14:68936000-68942600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr14:68936000-68942800	Weak transcription	HSMM	muscle
35	chr14:68936000-68943600	Weak transcription	Brain Hippocampus Middle	brain
36	chr14:68936000-68943600	Weak transcription	Esophagus	oesophagus
37	chr14:68936000-68947600	Weak transcription	Primary T cells from cord blood	blood
38	chr14:68936200-68938600	Weak transcription	Colon Smooth Muscle	Colon
39	chr14:68936200-68938800	Weak transcription	Lung	lung
40	chr14:68936200-68941200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr14:68936200-68942800	Weak transcription	Hela-S3	cervix
42	chr14:68936200-68943600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr14:68936200-68943600	Weak transcription	Brain Anterior Caudate	brain
44	chr14:68936400-68939000	Weak transcription	Stomach Mucosa	stomach
45	chr14:68936600-68938800	Weak transcription	Liver	Liver
46	chr14:68936600-68939400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr14:68936800-68940200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr14:68936800-68940200	Enhancers	H9 Cell Line	embryonic stem cell
49	chr14:68936800-68940200	Enhancers	Pancreas	Pancrea
50	chr14:68936800-68943400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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