Variant report

Variant	rs11802399
Chromosome Location	chr1:227353753-227353754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11799389	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800169	0.82[EUR][1000 genomes]
rs11800364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800959	1.00[ASN][1000 genomes]
rs11801012	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801282	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804181	0.82[EUR][1000 genomes]
rs11804807	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805012	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805662	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11806633	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806721	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs11807068	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs11807375	1.00[ASN][1000 genomes]
rs11807425	1.00[ASN][1000 genomes]
rs11807957	1.00[ASN][1000 genomes]
rs11808210	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11808670	1.00[ASN][1000 genomes]
rs11808674	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11809113	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809905	1.00[ASN][1000 genomes]
rs11810440	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11811210	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811620	1.00[ASN][1000 genomes]
rs11812048	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs12402400	1.00[ASN][1000 genomes]
rs12403978	1.00[ASN][1000 genomes]
rs12404219	1.00[ASN][1000 genomes]
rs1317490	1.00[ASN][1000 genomes]
rs16846842	1.00[GIH][hapmap]
rs16846989	1.00[GIH][hapmap]
rs17528049	1.00[ASN][1000 genomes]
rs17528077	1.00[ASN][1000 genomes]
rs1801783	1.00[ASN][1000 genomes]
rs34125608	1.00[ASN][1000 genomes]
rs35601687	1.00[ASN][1000 genomes]
rs41268741	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41268743	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270147	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41303131	1.00[ASN][1000 genomes]
rs45553032	1.00[ASN][1000 genomes]
rs55811522	1.00[ASN][1000 genomes]
rs56100227	1.00[ASN][1000 genomes]
rs61515455	1.00[ASN][1000 genomes]
rs61833999	1.00[ASN][1000 genomes]
rs61834000	1.00[ASN][1000 genomes]
rs61834003	1.00[ASN][1000 genomes]
rs61834008	1.00[ASN][1000 genomes]
rs61834038	1.00[ASN][1000 genomes]
rs66602251	1.00[ASN][1000 genomes]
rs6671926	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680937	1.00[ASN][1000 genomes]
rs73096355	1.00[ASN][1000 genomes]
rs73096357	1.00[ASN][1000 genomes]
rs7524967	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530155	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535648	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547092	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9660532	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv549270	chr1:227290139-227361072	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	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
9	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
10	esv33574	chr1:227349648-227354190	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11802399	CDC42BPA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227287400-227360800	Weak transcription	Psoas Muscle	Psoas
2	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:227317000-227374200	Weak transcription	HepG2	liver
5	chr1:227326600-227355200	Weak transcription	Small Intestine	intestine
6	chr1:227328000-227354400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:227328800-227354200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:227329600-227358400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:227329600-227380000	Weak transcription	Aorta	Aorta
10	chr1:227331600-227355000	Weak transcription	Brain Anterior Caudate	brain
11	chr1:227331600-227358400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:227332800-227354600	Weak transcription	Ovary	ovary
13	chr1:227333200-227354800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:227333400-227354000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:227333400-227354400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:227333400-227358400	Weak transcription	Osteobl	bone
17	chr1:227333400-227359000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:227333400-227381000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
20	chr1:227334800-227371800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:227339600-227354000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:227343200-227400400	Weak transcription	A549	lung
23	chr1:227343600-227358400	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:227346800-227354000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:227346800-227355000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:227346800-227357400	Weak transcription	Brain Substantia Nigra	brain
27	chr1:227346800-227357800	Weak transcription	NHDF-Ad	bronchial
28	chr1:227346800-227358000	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:227346800-227358200	Weak transcription	Right Ventricle	heart
30	chr1:227346800-227358400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:227346800-227366600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:227346800-227379800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:227346800-227403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
36	chr1:227347200-227378000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:227347800-227354200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:227347800-227357400	Weak transcription	Left Ventricle	heart
39	chr1:227347800-227363600	Weak transcription	Fetal Stomach	stomach
40	chr1:227347800-227385800	Weak transcription	Fetal Intestine Small	intestine
41	chr1:227347800-227390400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:227348000-227358200	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:227348000-227358400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:227348000-227361000	Weak transcription	NHEK	skin
45	chr1:227348200-227354400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:227348200-227354400	Weak transcription	Fetal Intestine Large	intestine
47	chr1:227348200-227357800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:227348200-227358000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:227348200-227358000	Weak transcription	HSMM	muscle
50	chr1:227348200-227358200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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