Variant report

Variant	rs1560214
Chromosome Location	chr7:128077817-128077818
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	MAFF	chr7:128077775-128078143	K562	blood:	n/a	n/a
2	WRNIP1	chr7:128077807-128077959	GM12878	blood:	n/a	n/a
3	MAFK	chr7:128077721-128078045	K562	blood:	n/a	n/a
4	CBX3	chr7:128077609-128077994	K562	blood:	n/a	n/a
5	GATA2	chr7:128077815-128078172	K562	blood:	n/a	chr7:128078005-128078012 chr7:128078005-128078012 chr7:128078000-128078016 chr7:128078005-128078012
6	SPI1	chr7:128077753-128078064	GM12891	blood:	n/a	chr7:128077947-128077960 chr7:128077948-128077961 chr7:128077925-128077938
7	TEAD4	chr7:128077653-128078221	K562	blood:	n/a	n/a
8	SPI1	chr7:128077603-128078242	HL-60	blood:	n/a	chr7:128077947-128077960 chr7:128077948-128077961 chr7:128077925-128077938

No.	Distal block	Cell Line	Cell type
1	chr7:128077598..128080477-chr7:128092228..128095663,3	K562	blood:
2	chr7:128048480..128050287-chr7:128075489..128078227,2	MCF-7	breast:
3	chr7:128077482..128079015-chr7:128094257..128096548,2	MCF-7	breast:
4	chr7:128071934..128079559-chr7:128081793..128086197,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228700	TF binding region
ENSG00000238590	Chromatin interaction
ENSG00000240758	Chromatin interaction
ENSG00000135245	Chromatin interaction
ENSG00000273184	Chromatin interaction
ENSG00000106348	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10229016	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10229394	1.00[CEU][hapmap];0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10230632	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10230965	1.00[JPT][hapmap]
rs10245559	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10251597	1.00[JPT][hapmap]
rs10271590	0.85[ASN][1000 genomes]
rs1035971	0.87[ASW][hapmap];0.82[LWK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs1065267	0.89[CEU][hapmap]
rs11770116	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[MKK][hapmap];0.80[AMR][1000 genomes]
rs11980741	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12672625	1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs13245629	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs17537088	0.83[CEU][hapmap]
rs2288548	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2288549	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2402892	0.88[TSI][hapmap]
rs2402895	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2562730	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562731	0.80[ASN][1000 genomes]
rs2562732	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2562733	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2562734	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562737	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2562740	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2732394	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732397	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2732429	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2732432	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28479078	0.85[ASN][1000 genomes]
rs3097361	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35586323	0.84[ASN][1000 genomes]
rs3958071	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4728108	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4731446	0.91[AMR][1000 genomes]
rs4731448	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4731450	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4731453	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4731454	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4731455	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5009156	0.85[ASN][1000 genomes]
rs58979384	0.85[ASN][1000 genomes]
rs6467178	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947697	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6948333	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6959839	0.82[AMR][1000 genomes]
rs7797240	0.89[ASN][1000 genomes]
rs930106	0.87[AMR][1000 genomes]

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	nsv831124	chr7:127970345-128147910	Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	esv1801356	chr7:128073366-128084133	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1560214	TMEM209	cis	parietal	SCAN
rs1560214	IL31RA	trans	parietal	SCAN
rs1560214	FAM71F2	cis	cerebellum	SCAN
rs1560214	ZNF800	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128051400-128086200	Weak transcription	Right Atrium	heart
2	chr7:128071800-128078600	Weak transcription	Adipose Nuclei	Adipose
3	chr7:128073800-128083800	Weak transcription	Esophagus	oesophagus
4	chr7:128075600-128083600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:128075600-128093800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:128075600-128093800	Weak transcription	Pancreas	Pancrea
7	chr7:128076000-128084000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr7:128076200-128080600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr7:128076200-128081800	Weak transcription	HepG2	liver
10	chr7:128076400-128079600	Enhancers	Primary B cells from peripheral blood	blood
11	chr7:128076400-128083400	Weak transcription	Placenta	Placenta
12	chr7:128076400-128083600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:128076400-128084000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr7:128077000-128079800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr7:128077400-128078400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr7:128077400-128078600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr7:128077600-128078000	Flanking Active TSS	GM12878-XiMat	blood
18	chr7:128077600-128078600	Enhancers	Primary hematopoietic stem cells	blood
19	chr7:128077600-128079400	Enhancers	K562	blood
20	chr7:128077800-128078200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr7:128077800-128078200	Active TSS	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links