Variant report

Variant	rs16845030
Chromosome Location	chr1:225727528-225727529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225726335..225728702-chr1:225730205..225734666,5	MCF-7	breast:
2	chr1:225725972..225727966-chr1:225729747..225732375,2	K562	blood:
3	chr1:225710178..225712804-chr1:225725363..225728293,2	MCF-7	breast:
4	chr1:225726738..225728808-chr1:225780265..225782118,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10495242	0.93[YRI][hapmap]
rs12032961	0.88[YRI][hapmap]
rs12034829	0.93[YRI][hapmap]
rs12564648	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564687	0.89[EUR][1000 genomes]
rs12564945	0.87[ASN][1000 genomes]
rs12565399	0.84[EUR][1000 genomes]
rs12566165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567909	0.95[ASN][1000 genomes]
rs12568642	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16845040	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];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1771316	1.00[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1841655	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1891000	1.00[YRI][hapmap]
rs2657568	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2840960	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs499782	0.86[YRI][hapmap]
rs55689260	0.82[ASN][1000 genomes]
rs55899644	0.89[EUR][1000 genomes]
rs56250189	0.81[EUR][1000 genomes]
rs58088270	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6665838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7544335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];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:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225701400-225744400	Weak transcription	HUVEC	blood vessel
2	chr1:225701400-225747000	Weak transcription	Hela-S3	cervix
3	chr1:225705600-225747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:225707200-225755000	Weak transcription	Gastric	stomach
5	chr1:225712400-225729600	Weak transcription	Right Ventricle	heart
6	chr1:225714800-225729600	Weak transcription	Ovary	ovary
7	chr1:225717600-225732000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:225717600-225744400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:225717800-225729600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:225717800-225744400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:225717800-225745000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:225717800-225747400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:225717800-225747400	Weak transcription	Fetal Stomach	stomach
14	chr1:225717800-225758200	Weak transcription	HepG2	liver
15	chr1:225718400-225732600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:225718400-225756400	Weak transcription	NHLF	lung
17	chr1:225719000-225728000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:225719800-225730400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr1:225721000-225728600	Weak transcription	Fetal Brain Male	brain
20	chr1:225721600-225735200	Weak transcription	HSMM	muscle
21	chr1:225722000-225729800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:225722800-225728000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:225722800-225747600	Weak transcription	Fetal Intestine Small	intestine
24	chr1:225723000-225728200	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:225723200-225739600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:225723400-225735200	Weak transcription	NH-A	brain
27	chr1:225724600-225728800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr1:225724800-225728400	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr1:225725000-225727600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr1:225725000-225727600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:225725200-225727600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr1:225725200-225727600	Enhancers	Brain Substantia Nigra	brain
33	chr1:225725200-225728400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:225725200-225728400	Enhancers	Fetal Lung	lung
35	chr1:225725400-225728800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr1:225725600-225729600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:225725800-225729200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:225725800-225730200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:225726000-225732000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:225726400-225727600	Enhancers	Psoas Muscle	Psoas
41	chr1:225726400-225728800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:225726400-225728800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:225726600-225727600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:225726600-225727600	Enhancers	Brain Angular Gyrus	brain
45	chr1:225726600-225727600	Enhancers	NHDF-Ad	bronchial
46	chr1:225726600-225727600	Enhancers	NHEK	skin
47	chr1:225726600-225728000	Enhancers	Primary B cells from peripheral blood	blood
48	chr1:225726600-225728200	Enhancers	A549	lung
49	chr1:225726600-225730200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:225726600-225730200	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links