Variant report

Variant	rs11803651
Chromosome Location	chr1:227471650-227471651
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227468377..227470578-chr1:227471178..227474571,3	K562	blood:
2	chr1:227339177..227341705-chr1:227470311..227471926,2	K562	blood:
3	chr1:227461391..227464005-chr1:227469962..227472348,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF678-5	chr1:227469373-227472002	l_204_chr1:227466302-227471954_brain

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11800169	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801282	0.85[EUR][1000 genomes]
rs11804181	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806721	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11807068	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11807375	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11807425	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11807957	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11808210	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11808670	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11808674	0.87[EUR][1000 genomes]
rs11809905	0.87[EUR][1000 genomes]
rs11811620	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11812048	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35601687	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36055753	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270147	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6671926	0.82[AMR][1000 genomes]
rs7530155	0.89[EUR][1000 genomes]
rs7547092	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9660532	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	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
5	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
6	esv3453491	chr1:227462942-227482283	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv3453492	chr1:227462956-227482280	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11803651	CDC42BPA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
2	chr1:227443400-227474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:227447200-227473600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:227449600-227473600	Weak transcription	NH-A	brain
5	chr1:227458800-227472200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:227462600-227473600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:227462600-227500200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:227463000-227473000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:227464400-227472800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:227464400-227472800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:227465400-227472200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:227466200-227473200	Weak transcription	A549	lung
13	chr1:227466800-227472400	Weak transcription	Fetal Intestine Large	intestine
14	chr1:227467000-227472600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:227467200-227485800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:227468600-227472600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:227469000-227473000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:227469200-227473200	Weak transcription	HUVEC	blood vessel
19	chr1:227469200-227473600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:227469200-227477600	Weak transcription	Psoas Muscle	Psoas
21	chr1:227469200-227500200	Weak transcription	Left Ventricle	heart
22	chr1:227469200-227502600	Weak transcription	HSMM	muscle
23	chr1:227469400-227472200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:227469400-227472600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:227469400-227473200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:227469400-227477000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:227469600-227472000	Weak transcription	Right Ventricle	heart
28	chr1:227469600-227472400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:227469600-227472400	Weak transcription	Right Atrium	heart
30	chr1:227469600-227473000	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:227469600-227473200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:227469600-227473400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:227469600-227473600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:227469600-227473600	Weak transcription	Aorta	Aorta
35	chr1:227469600-227501800	Weak transcription	Fetal Stomach	stomach
36	chr1:227470600-227472200	Weak transcription	K562	blood
37	chr1:227470600-227473200	Weak transcription	Fetal Lung	lung
38	chr1:227470600-227483000	Weak transcription	Stomach Mucosa	stomach
39	chr1:227470600-227485800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:227470800-227472200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:227471400-227471800	ZNF genes & repeats	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links