Variant report

Variant	rs1988734
Chromosome Location	chr8:125578993-125578994
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NRF1	chr8:125578852-125579044	GM12878	blood:	n/a	n/a
2	POLR2A	chr8:125578700-125579141	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr8:125578853-125579027	HepG2	liver:	n/a	n/a
4	POLR2A	chr8:125578735-125579282	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:125573757..125577202-chr8:125578987..125583404,3	MCF-7	breast:
2	chr8:125572972..125577628-chr8:125578200..125582090,6	MCF-7	breast:
3	chr8:125572673..125575871-chr8:125577015..125582400,6	K562	blood:
4	chr8:125577321..125579071-chr8:125580874..125582837,2	MCF-7	breast:
5	chr8:125551552..125553200-chr8:125577686..125580051,3	K562	blood:
6	chr8:125577831..125580093-chr8:125580434..125583329,2	MCF-7	breast:

No data

Variant related genes	Relation type
MTSS1	TF binding region
ENSG00000170873	Chromatin interaction
ENSG00000147687	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10099060	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10103765	0.81[EUR][1000 genomes]
rs10505445	0.86[GIH][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs11778063	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11779706	0.84[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3763539	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3793399	0.90[GIH][hapmap]
rs3857943	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3857944	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4870903	0.90[GIH][hapmap]
rs4871501	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6470249	0.90[GIH][hapmap]
rs6470251	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6470252	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6991135	0.80[EUR][1000 genomes]
rs7001375	0.86[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs7821505	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7824951	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7828897	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7838223	0.84[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8180920	0.85[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8180922	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8180993	0.85[CEU][hapmap];0.84[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv525649	chr8:125565328-125600818	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1024804	chr8:125575803-125600950	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1025014	chr8:125578314-125600950	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125553800-125581200	Strong transcription	Fetal Brain Female	brain
2	chr8:125566000-125602400	Weak transcription	Aorta	Aorta
3	chr8:125566200-125590400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:125566400-125600600	Weak transcription	NHEK	skin
5	chr8:125566800-125581400	Weak transcription	HSMM	muscle
6	chr8:125567000-125590200	Weak transcription	Fetal Brain Male	brain
7	chr8:125570000-125584800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr8:125570800-125605000	Weak transcription	Colon Smooth Muscle	Colon
9	chr8:125571800-125581200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr8:125574400-125609400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr8:125574800-125580600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:125574800-125581000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr8:125574800-125590200	Weak transcription	HMEC	breast
14	chr8:125575400-125589200	Weak transcription	Esophagus	oesophagus
15	chr8:125575600-125600600	Weak transcription	Fetal Kidney	kidney
16	chr8:125575800-125581000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr8:125575800-125589200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr8:125576400-125583200	Weak transcription	Pancreas	Pancrea
19	chr8:125576600-125579200	Genic enhancers	Liver	Liver
20	chr8:125576600-125583600	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr8:125576600-125591400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr8:125576800-125590200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr8:125576800-125598200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr8:125577000-125579000	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr8:125577200-125579800	Weak transcription	Psoas Muscle	Psoas
26	chr8:125577200-125580600	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr8:125577200-125581200	Weak transcription	Right Ventricle	heart
28	chr8:125577200-125581800	Strong transcription	Brain Germinal Matrix	brain
29	chr8:125577200-125591400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr8:125577400-125579000	Enhancers	HUVEC	blood vessel
31	chr8:125577400-125579200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr8:125577400-125579800	Enhancers	Primary T cells fromperipheralblood	blood
33	chr8:125577400-125582000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr8:125577400-125586600	Weak transcription	Brain Angular Gyrus	brain
35	chr8:125577400-125589800	Weak transcription	NHLF	lung
36	chr8:125577600-125579200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr8:125577600-125579200	Enhancers	Primary T cells from cord blood	blood
38	chr8:125577600-125579200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr8:125577600-125579400	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr8:125577600-125579600	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr8:125577600-125579600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr8:125577600-125580800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr8:125577600-125582400	Strong transcription	Fetal Intestine Large	intestine
44	chr8:125577600-125586600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr8:125577600-125591600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr8:125577800-125579200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr8:125577800-125579400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr8:125577800-125589600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr8:125577800-125590000	Weak transcription	Osteobl	bone
50	chr8:125578000-125579000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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