Variant report

Variant	rs7245981
Chromosome Location	chr19:38187583-38187584
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	MYC	chr19:38187482-38187658	MCF-7	breast:	n/a	n/a
2	POLR2A	chr19:38187450-38187791	MCF-7	breast:	n/a	n/a
3	POLR2A	chr19:38187410-38188087	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr19:38187550-38187835	MCF-7	breast:	n/a	n/a
5	POLR2A	chr19:38187579-38187713	K562	blood:	n/a	n/a
6	POLR2A	chr19:38187496-38187783	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr19:38187453-38187774	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38134173..38137861-chr19:38186479..38189500,3	K562	blood:

Variant related genes	Relation type
ZNF781	TF binding region
ZFP30	TF binding region
ENSG00000267319	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10153500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1038084	0.95[YRI][hapmap]
rs10407657	0.95[YRI][hapmap]
rs10424047	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10424612	0.95[YRI][hapmap]
rs11083424	1.00[CEU][hapmap];0.84[YRI][hapmap]
rs11878261	0.81[EUR][1000 genomes]
rs11879149	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11880056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880604	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11883255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2075282	1.00[JPT][hapmap]
rs2927743	0.85[YRI][hapmap]
rs2927744	1.00[YRI][hapmap]
rs34206817	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34743484	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3810359	0.82[ASN][1000 genomes]
rs45505797	0.83[EUR][1000 genomes]
rs4802069	1.00[YRI][hapmap]
rs4803216	0.95[YRI][hapmap]
rs56075341	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56264690	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56281742	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57504517	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57725815	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57867853	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59966837	1.00[EUR][1000 genomes]
rs60686304	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62108260	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62108262	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62108264	0.82[ASN][1000 genomes]
rs62108289	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62108290	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62108292	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62108293	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62108297	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62108302	0.83[ASN][1000 genomes]
rs62108344	0.90[AFR][1000 genomes]
rs62108348	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62108350	0.82[ASN][1000 genomes]
rs62108354	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62110178	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62110183	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62110185	0.93[EUR][1000 genomes]
rs62110186	0.93[EUR][1000 genomes]
rs62110187	0.84[EUR][1000 genomes]
rs62110188	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62111488	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62111490	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7247175	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7255283	0.95[YRI][hapmap]
rs7258992	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7259029	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7259272	0.88[CHB][hapmap]
rs7259717	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73930999	0.83[EUR][1000 genomes]
rs73932929	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73932955	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8101991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8102189	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8104124	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8104747	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8108261	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8113076	0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv978813	chr19:38187175-38188871	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38183200-38208800	Weak transcription	Fetal Heart	heart
2	chr19:38183400-38188800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr19:38183400-38190000	Weak transcription	Stomach Mucosa	stomach
4	chr19:38183600-38187600	Weak transcription	Primary T cells from cord blood	blood
5	chr19:38183600-38187600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:38183600-38187600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:38183600-38187800	Weak transcription	Primary B cells from cord blood	blood
8	chr19:38183600-38187800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:38183600-38188000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:38183600-38188800	Weak transcription	Fetal Kidney	kidney
11	chr19:38183600-38189400	Weak transcription	Psoas Muscle	Psoas
12	chr19:38183600-38190000	Weak transcription	Small Intestine	intestine
13	chr19:38183800-38187600	Weak transcription	Placenta	Placenta
14	chr19:38183800-38187600	Weak transcription	Fetal Thymus	thymus
15	chr19:38184200-38187600	Weak transcription	HSMMtube	muscle
16	chr19:38184200-38187800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:38184200-38188600	Weak transcription	Fetal Brain Male	brain
18	chr19:38184200-38201200	Weak transcription	Colonic Mucosa	Colon
19	chr19:38184400-38187800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:38184400-38208800	Weak transcription	HepG2	liver
21	chr19:38186400-38191200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
22	chr19:38186800-38189200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr19:38186800-38189800	Strong transcription	Fetal Stomach	stomach
24	chr19:38186800-38191200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:38187000-38207800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:38187000-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:38187200-38187800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr19:38187200-38190800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:38187200-38191600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:38187400-38187600	Genic enhancers	H1 Cell Line	embryonic stem cell
31	chr19:38187400-38187600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr19:38187400-38187600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr19:38187400-38187600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:38187400-38187600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
35	chr19:38187400-38187600	Strong transcription	Fetal Muscle Leg	muscle
36	chr19:38187400-38187800	Strong transcription	Brain Hippocampus Middle	brain
37	chr19:38187400-38187800	ZNF genes & repeats	Fetal Intestine Large	intestine
38	chr19:38187400-38187800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
39	chr19:38187400-38188000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr19:38187400-38188000	ZNF genes & repeats	Pancreas	Pancrea
41	chr19:38187400-38188000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
42	chr19:38187400-38188200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:38187400-38188200	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr19:38187400-38188200	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:38187400-38188200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
46	chr19:38187400-38188200	Strong transcription	Right Ventricle	heart
47	chr19:38187400-38188200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
48	chr19:38187400-38188200	ZNF genes & repeats	Spleen	Spleen
49	chr19:38187400-38188400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:38187400-38188400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links