Variant report

Variant	rs7541650
Chromosome Location	chr1:180660887-180660888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180657321..180662997-chr1:180672435..180676141,5	K562	blood:
2	chr1:180659309..180661145-chr1:180702429..180704550,2	MCF-7	breast:
3	chr1:180659868..180662316-chr1:180673434..180676227,3	K562	blood:
4	chr1:180659367..180662219-chr1:180675558..180677595,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10914061	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10914096	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs12118646	0.83[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap];0.84[LWK][hapmap];0.88[TSI][hapmap]
rs1339768	0.86[CHB][hapmap];0.84[CHD][hapmap];0.86[ASN][1000 genomes]
rs1970404	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs2331626	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs3002114	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs3002117	0.86[ASN][1000 genomes]
rs3002123	0.86[CHB][hapmap];0.86[CHD][hapmap];0.88[ASN][1000 genomes]
rs3013633	0.86[ASN][1000 genomes]
rs3013634	0.85[ASN][1000 genomes]
rs3789366	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs3843278	0.86[CHB][hapmap];0.97[ASN][1000 genomes]
rs3845406	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs3856058	0.90[CHB][hapmap];0.92[ASN][1000 genomes]
rs3897798	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651073	0.87[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap]
rs6659049	0.86[CHB][hapmap]
rs6659368	0.86[ASN][1000 genomes]
rs6661105	0.81[CHB][hapmap]
rs7524547	0.94[ASN][1000 genomes]
rs9425881	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs9970145	0.81[CHB][hapmap]
rs9970363	0.80[CHB][hapmap]

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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2754432	chr1:180645343-180692343	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180633200-180672000	Weak transcription	K562	blood
2	chr1:180640200-180662200	Weak transcription	Fetal Heart	heart
3	chr1:180641200-180662800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:180641600-180661200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:180644000-180662600	Weak transcription	Left Ventricle	heart
6	chr1:180644000-180663800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:180646400-180662200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:180647400-180662600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:180647600-180661200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:180648000-180663800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:180649000-180666200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:180650200-180665600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:180650200-180669800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:180652000-180661000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:180652000-180672400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:180659000-180661800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:180659400-180661200	Enhancers	A549	lung
18	chr1:180659400-180661400	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:180659400-180661400	Enhancers	Rectal Smooth Muscle	rectum
20	chr1:180659400-180661600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:180659600-180661600	Enhancers	Fetal Brain Female	brain
22	chr1:180659800-180661800	Enhancers	Fetal Brain Male	brain
23	chr1:180660200-180661000	Enhancers	HUVEC	blood vessel
24	chr1:180660200-180661200	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:180660400-180661000	Enhancers	Hela-S3	cervix
26	chr1:180660400-180661000	Enhancers	Osteobl	bone
27	chr1:180660400-180661600	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:180660400-180661600	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr1:180660400-180662400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr1:180660600-180661000	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr1:180660600-180661000	Enhancers	Aorta	Aorta
32	chr1:180660600-180661000	Enhancers	Fetal Kidney	kidney
33	chr1:180660600-180661400	Enhancers	Brain Angular Gyrus	brain
34	chr1:180660600-180661400	Enhancers	Right Ventricle	heart
35	chr1:180660600-180661600	Enhancers	Fetal Lung	lung
36	chr1:180660800-180661600	Enhancers	Brain Germinal Matrix	brain
37	chr1:180660800-180662600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:180660800-180664200	Enhancers	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links