Variant report

Variant	rs7547092
Chromosome Location	chr1:227413438-227413439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227396969..227399919-chr1:227412592..227414970,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11799389	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800169	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11800364	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800959	1.00[ASN][1000 genomes]
rs11801012	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801282	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802399	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803651	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11804181	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11804807	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11805012	1.00[ASN][1000 genomes]
rs11806633	1.00[ASN][1000 genomes]
rs11806721	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807068	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807375	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807425	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807957	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808210	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808670	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808674	1.00[CEU][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809113	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809905	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810440	1.00[CEU][hapmap]
rs11811210	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811620	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811982	1.00[ASN][1000 genomes]
rs11812048	1.00[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34125608	1.00[ASN][1000 genomes]
rs35601687	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36055753	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41268741	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41268743	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270147	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671926	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73096355	1.00[ASN][1000 genomes]
rs73096357	1.00[ASN][1000 genomes]
rs7524967	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7530155	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535648	1.00[ASN][1000 genomes]
rs9660532	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	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
rs7547092	CDC42BPA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227370000-227413600	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr1:227380200-227421800	Weak transcription	Ovary	ovary
3	chr1:227382000-227414000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:227383600-227421800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
6	chr1:227386400-227413800	Weak transcription	Brain Anterior Caudate	brain
7	chr1:227387000-227413600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:227387400-227414000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:227390600-227413600	Weak transcription	Small Intestine	intestine
10	chr1:227396800-227413600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:227398200-227413600	Weak transcription	NHLF	lung
12	chr1:227398800-227413800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:227399400-227415400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:227400400-227426800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:227402400-227430600	Weak transcription	Pancreas	Pancrea
16	chr1:227404000-227413800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:227405600-227421800	Weak transcription	Gastric	stomach
18	chr1:227406400-227417200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:227407200-227432400	Weak transcription	Right Ventricle	heart
20	chr1:227408000-227413600	Weak transcription	Left Ventricle	heart
21	chr1:227408400-227415200	Weak transcription	Fetal Kidney	kidney
22	chr1:227410800-227413600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:227411000-227413600	Weak transcription	Psoas Muscle	Psoas
24	chr1:227411200-227413800	Weak transcription	Brain Substantia Nigra	brain
25	chr1:227411600-227413600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:227411600-227413800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:227411600-227413800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:227411800-227413600	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:227411800-227413600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:227411800-227430600	Weak transcription	Right Atrium	heart
31	chr1:227411800-227431400	Weak transcription	Fetal Intestine Small	intestine
32	chr1:227412600-227414200	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr1:227412800-227413600	Enhancers	Osteobl	bone
34	chr1:227412800-227414600	Enhancers	Stomach Mucosa	stomach
35	chr1:227413000-227414000	Enhancers	NH-A	brain
36	chr1:227413000-227414200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:227413000-227414200	Enhancers	Hela-S3	cervix
38	chr1:227413000-227414400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:227413000-227414400	Enhancers	NHEK	skin
40	chr1:227413200-227414000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:227413200-227414000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:227413200-227414000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:227413200-227414000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:227413200-227414200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:227413200-227414200	Enhancers	HSMM	muscle
46	chr1:227413200-227414200	Flanking Active TSS	HUVEC	blood vessel
47	chr1:227413200-227414200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr1:227413400-227413600	Enhancers	K562	blood
49	chr1:227413400-227413600	Enhancers	NHDF-Ad	bronchial
50	chr1:227413400-227413800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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