Variant report

Variant	rs7525538
Chromosome Location	chr1:78054898-78054899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:78053952..78055571-chr1:78057037..78059846,2	MCF-7	breast:
2	chr1:78049428..78052334-chr1:78052649..78055107,2	MCF-7	breast:
3	chr1:78054448..78057258-chr1:78101287..78103947,2	K562	blood:
4	chr1:78053424..78055384-chr1:78055842..78057963,2	K562	blood:
5	chr1:78052836..78055069-chr1:78065694..78068247,2	K562	blood:

Variant related genes	Relation type
ENSG00000036549	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs17100817	0.93[EUR][1000 genomes]
rs17100819	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1874816	1.00[CEU][hapmap]
rs34351666	0.87[EUR][1000 genomes]
rs34974859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41313399	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61777073	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs61784760	1.00[AFR][1000 genomes]
rs6603957	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6659285	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6660964	1.00[CEU][hapmap]
rs6662245	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6677011	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6678173	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6701361	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7532455	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7546155	1.00[EUR][1000 genomes]
rs7546605	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7550587	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7555421	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7555864	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[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	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3337461	chr1:78036000-78153859	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78006200-78064400	Weak transcription	Stomach Mucosa	stomach
2	chr1:78024800-78071000	Weak transcription	Gastric	stomach
3	chr1:78032000-78062800	Weak transcription	Fetal Heart	heart
4	chr1:78032600-78070800	Weak transcription	Aorta	Aorta
5	chr1:78032800-78070600	Weak transcription	Small Intestine	intestine
6	chr1:78033000-78057000	Weak transcription	Spleen	Spleen
7	chr1:78033000-78057200	Weak transcription	Psoas Muscle	Psoas
8	chr1:78033200-78072600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:78033400-78057600	Weak transcription	Right Ventricle	heart
10	chr1:78033400-78069600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:78033600-78070800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:78034000-78056200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:78037800-78055400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:78038600-78071000	Weak transcription	Pancreas	Pancrea
15	chr1:78039000-78070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:78042000-78070800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:78042000-78074600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:78042200-78073800	Weak transcription	Fetal Brain Female	brain
19	chr1:78043000-78070200	Weak transcription	Brain Substantia Nigra	brain
20	chr1:78044200-78055200	Weak transcription	Ovary	ovary
21	chr1:78044200-78069000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:78044400-78063000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:78046400-78056000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:78047000-78056000	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:78047000-78070800	Weak transcription	Lung	lung
26	chr1:78047000-78071200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:78047600-78056200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:78047600-78056600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:78047600-78056800	Weak transcription	K562	blood
30	chr1:78047600-78060200	Weak transcription	HUVEC	blood vessel
31	chr1:78047600-78061800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:78047600-78062200	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:78047600-78063000	Weak transcription	Fetal Brain Male	brain
34	chr1:78047600-78063200	Weak transcription	Brain Anterior Caudate	brain
35	chr1:78047600-78069000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:78047600-78070800	Weak transcription	HSMMtube	muscle
37	chr1:78047600-78071000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr1:78047600-78071600	Weak transcription	Thymus	Thymus
39	chr1:78047600-78072400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:78047600-78072600	Weak transcription	Fetal Kidney	kidney
41	chr1:78047600-78074600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr1:78047600-78074800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:78047600-78085600	Weak transcription	NHLF	lung
44	chr1:78047800-78055000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:78047800-78058600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:78047800-78061800	Weak transcription	HSMM	muscle
47	chr1:78047800-78063000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:78047800-78063200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:78047800-78063200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:78047800-78070800	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links