Variant report

Variant	rs41270147
Chromosome Location	chr1:227406908-227406909
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227405924..227407789-chr1:227409135..227411231,2	K562	blood:
2	chr1:227402647..227405396-chr1:227406531..227409406,3	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11799389	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800169	0.93[EUR][1000 genomes]
rs11800364	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800959	1.00[ASN][1000 genomes]
rs11801012	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801282	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802399	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803651	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11804181	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11804807	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805012	1.00[ASN][1000 genomes]
rs11806633	1.00[ASN][1000 genomes]
rs11806721	1.00[ASN][1000 genomes]
rs11807068	1.00[ASN][1000 genomes]
rs11807375	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807425	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807957	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808210	1.00[ASN][1000 genomes]
rs11808670	1.00[ASN][1000 genomes]
rs11808674	1.00[ASN][1000 genomes]
rs11809113	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809905	1.00[ASN][1000 genomes]
rs11811210	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811620	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811982	1.00[ASN][1000 genomes]
rs11812048	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34125608	1.00[ASN][1000 genomes]
rs35601687	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36055753	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs41268741	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41268743	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56100227	1.00[ASN][1000 genomes]
rs61515455	1.00[ASN][1000 genomes]
rs61834038	1.00[ASN][1000 genomes]
rs66602251	1.00[ASN][1000 genomes]
rs6671926	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73096355	1.00[ASN][1000 genomes]
rs73096357	1.00[ASN][1000 genomes]
rs7524967	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530155	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535648	1.00[ASN][1000 genomes]
rs7547092	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9660532	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41270147	CDC42BPA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227348200-227408400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr1:227348200-227412200	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:227370000-227413600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:227375600-227410800	Weak transcription	HepG2	liver
5	chr1:227376600-227412600	Weak transcription	Fetal Lung	lung
6	chr1:227380200-227421800	Weak transcription	Ovary	ovary
7	chr1:227382000-227414000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:227383600-227421800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
10	chr1:227386400-227413800	Weak transcription	Brain Anterior Caudate	brain
11	chr1:227387000-227413600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:227387400-227414000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:227390600-227413600	Weak transcription	Small Intestine	intestine
14	chr1:227396800-227413600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:227398200-227413600	Weak transcription	NHLF	lung
16	chr1:227398600-227407000	Weak transcription	Lung	lung
17	chr1:227398800-227407000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:227398800-227411200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:227398800-227413800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:227399000-227408800	Weak transcription	Liver	Liver
21	chr1:227399200-227407000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:227399400-227411200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:227399400-227415400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:227399600-227413200	Weak transcription	HSMM	muscle
25	chr1:227399800-227407000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:227399800-227411000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:227400400-227407600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:227400400-227408200	Weak transcription	K562	blood
29	chr1:227400400-227410800	Weak transcription	Brain Angular Gyrus	brain
30	chr1:227400400-227410800	Weak transcription	Brain Substantia Nigra	brain
31	chr1:227400400-227413000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:227400400-227413000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:227400400-227426800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:227400600-227413000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:227400600-227413000	Weak transcription	NHEK	skin
36	chr1:227400800-227412800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:227401400-227407000	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:227401600-227413400	Weak transcription	A549	lung
39	chr1:227402400-227410800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:227402400-227430600	Weak transcription	Pancreas	Pancrea
41	chr1:227403000-227407200	Weak transcription	Fetal Heart	heart
42	chr1:227403800-227412800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:227404000-227413800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:227404400-227412800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:227405600-227407000	Weak transcription	Left Ventricle	heart
46	chr1:227405600-227407600	Enhancers	Stomach Mucosa	stomach
47	chr1:227405600-227408200	Weak transcription	Psoas Muscle	Psoas
48	chr1:227405600-227421800	Weak transcription	Gastric	stomach
49	chr1:227406400-227417200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:227406600-227407000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links