Variant report

Variant	rs7548206
Chromosome Location	chr1:225756233-225756234
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225746985..225751093-chr1:225752796..225757571,6	MCF-7	breast:
2	chr1:225754769..225757608-chr1:225839497..225842877,3	MCF-7	breast:
3	chr1:225754514..225756572-chr1:225964591..225966277,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12564648	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12564687	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12564945	0.85[ASN][1000 genomes]
rs12565399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12566165	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12567909	0.93[ASN][1000 genomes]
rs12568642	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16845030	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16845040	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500644	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1771316	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1841655	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2657568	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840960	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55689260	0.80[ASN][1000 genomes]
rs55899644	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56250189	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58088270	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225717800-225758200	Weak transcription	HepG2	liver
2	chr1:225718400-225756400	Weak transcription	NHLF	lung
3	chr1:225730600-225765800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:225730600-225776200	Weak transcription	Pancreas	Pancrea
5	chr1:225732400-225763000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:225734600-225763600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:225737800-225756400	Weak transcription	Right Ventricle	heart
8	chr1:225738600-225758000	Weak transcription	Brain Germinal Matrix	brain
9	chr1:225741800-225758600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:225744800-225759400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:225744800-225760200	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:225744800-225761400	Weak transcription	Brain Angular Gyrus	brain
13	chr1:225744800-225768200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:225744800-225768600	Weak transcription	Fetal Brain Male	brain
15	chr1:225745000-225760800	Weak transcription	Fetal Kidney	kidney
16	chr1:225745000-225770000	Weak transcription	HUVEC	blood vessel
17	chr1:225745000-225772800	Weak transcription	Fetal Brain Female	brain
18	chr1:225746600-225756400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:225747200-225759800	Weak transcription	Brain Substantia Nigra	brain
20	chr1:225747800-225756400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:225747800-225765000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:225748400-225759800	Weak transcription	Brain Anterior Caudate	brain
23	chr1:225748800-225765800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:225748800-225799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:225749200-225783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:225750000-225758000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:225750800-225761200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:225751800-225759800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:225752200-225758800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:225753600-225758000	Weak transcription	Fetal Intestine Small	intestine
31	chr1:225753600-225758800	Weak transcription	Lung	lung
32	chr1:225753800-225759200	Weak transcription	Psoas Muscle	Psoas
33	chr1:225754000-225759600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:225754000-225764600	Weak transcription	Fetal Stomach	stomach
35	chr1:225754200-225756400	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:225754200-225756400	Weak transcription	A549	lung
37	chr1:225754200-225756600	Weak transcription	NHEK	skin
38	chr1:225754200-225757800	Weak transcription	Hela-S3	cervix
39	chr1:225754200-225761000	Weak transcription	Aorta	Aorta
40	chr1:225754200-225764400	Weak transcription	Right Atrium	heart
41	chr1:225754200-225764600	Weak transcription	Ovary	ovary
42	chr1:225754400-225756400	Weak transcription	NHDF-Ad	bronchial
43	chr1:225754400-225760000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:225754400-225764400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:225754400-225769400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:225754600-225761200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:225754600-225764400	Weak transcription	Fetal Muscle Leg	muscle
48	chr1:225754600-225766000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:225754800-225759800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:225754800-225760200	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links