Variant report

Variant	rs16845040
Chromosome Location	chr1:225754079-225754080
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225749504..225751899-chr1:225752062..225754105,2	MCF-7	breast:
2	chr1:225746985..225751093-chr1:225752796..225757571,6	MCF-7	breast:
3	chr1:225751371..225754365-chr1:225954697..225956574,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10495242	0.92[YRI][hapmap]
rs12034829	0.92[YRI][hapmap]
rs12564648	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12564687	0.94[EUR][1000 genomes]
rs12564945	0.85[ASN][1000 genomes]
rs12565399	0.89[EUR][1000 genomes]
rs12566165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12567909	0.93[ASN][1000 genomes]
rs12568642	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16845030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17500644	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1771316	0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1841655	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1891000	1.00[YRI][hapmap]
rs2657568	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840960	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs499782	0.83[YRI][hapmap]
rs55689260	0.80[ASN][1000 genomes]
rs55899644	0.94[EUR][1000 genomes]
rs56250189	0.86[EUR][1000 genomes]
rs58088270	0.89[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[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7548206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[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:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225707200-225755000	Weak transcription	Gastric	stomach
2	chr1:225717800-225758200	Weak transcription	HepG2	liver
3	chr1:225718400-225756400	Weak transcription	NHLF	lung
4	chr1:225730600-225765800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:225730600-225776200	Weak transcription	Pancreas	Pancrea
6	chr1:225732400-225763000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:225734600-225763600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:225736600-225756200	Weak transcription	HSMMtube	muscle
9	chr1:225737800-225756400	Weak transcription	Right Ventricle	heart
10	chr1:225738600-225758000	Weak transcription	Brain Germinal Matrix	brain
11	chr1:225741800-225758600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:225744800-225759400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:225744800-225760200	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:225744800-225761400	Weak transcription	Brain Angular Gyrus	brain
15	chr1:225744800-225768200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:225744800-225768600	Weak transcription	Fetal Brain Male	brain
17	chr1:225745000-225760800	Weak transcription	Fetal Kidney	kidney
18	chr1:225745000-225770000	Weak transcription	HUVEC	blood vessel
19	chr1:225745000-225772800	Weak transcription	Fetal Brain Female	brain
20	chr1:225745400-225755800	Weak transcription	Fetal Intestine Large	intestine
21	chr1:225745800-225755000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:225746200-225756200	Weak transcription	Fetal Heart	heart
23	chr1:225746600-225755600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:225746600-225756400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:225747200-225759800	Weak transcription	Brain Substantia Nigra	brain
26	chr1:225747800-225755400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:225747800-225755800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:225747800-225756400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:225747800-225765000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:225748400-225759800	Weak transcription	Brain Anterior Caudate	brain
31	chr1:225748600-225756200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:225748800-225765800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:225748800-225799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:225749200-225783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:225749400-225755200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:225749400-225755400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:225750000-225758000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:225750800-225761200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:225751000-225754800	Strong transcription	NH-A	brain
40	chr1:225751800-225754400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr1:225751800-225759800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:225752200-225758800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr1:225752800-225755200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:225753200-225754200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:225753200-225755200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:225753400-225754200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:225753400-225754200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:225753400-225754200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:225753400-225754200	Genic enhancers	Fetal Muscle Leg	muscle
50	chr1:225753400-225754200	Genic enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links