Variant report

Variant	rs3768423
Chromosome Location	chr1:227177293-227177294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:227177150-227177336	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr1:227176913-227177335	K562	blood:	n/a	n/a
3	POLR2A	chr1:227176707-227177612	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:227169948-227179599	K562	blood:	n/a	n/a
5	POLR2A	chr1:227176781-227177361	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227127714..227130249-chr1:227177075..227179669,4	K562	blood:
2	chr1:227176748..227179639-chr1:227203696..227206126,2	K562	blood:
3	chr1:227176058..227178515-chr1:227186795..227190068,3	MCF-7	breast:
4	chr1:227126152..227130822-chr1:227174735..227178540,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000233706	TF binding region
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1045285	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045286	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1045287	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045289	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1045290	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10495273	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10916075	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577007	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578103	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11578479	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11580229	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11583229	0.89[ASN][1000 genomes]
rs11586604	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11587443	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11588904	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11589344	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1186	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12403236	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12405857	0.89[ASN][1000 genomes]
rs12406714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409230	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12409428	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409755	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12410103	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12593	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1343743	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1343744	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1343745	0.99[ASN][1000 genomes]
rs17528667	0.86[AMR][1000 genomes]
rs17592479	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17600627	0.85[AMR][1000 genomes]
rs17600669	0.86[AMR][1000 genomes]
rs17600725	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17600747	0.89[ASN][1000 genomes]
rs17600947	0.89[ASN][1000 genomes]
rs1929862	0.87[AMR][1000 genomes]
rs1929863	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1929864	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2104860	0.91[ASN][1000 genomes]
rs2183836	0.85[AFR][1000 genomes]
rs2297415	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2297416	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2297418	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297419	0.99[ASN][1000 genomes]
rs3738725	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3738729	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768419	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768420	0.96[ASN][1000 genomes]
rs3768421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3768424	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3768425	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3795445	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795446	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795449	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795451	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3795453	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61834001	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61834004	0.86[AMR][1000 genomes]
rs61834005	0.81[AMR][1000 genomes]
rs61834006	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs61834039	0.89[ASN][1000 genomes]
rs6426558	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6426559	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6426560	0.89[ASN][1000 genomes]
rs6659424	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6664955	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670924	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6684821	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690803	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6693535	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6699400	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6704144	0.86[AMR][1000 genomes]
rs68087483	0.86[AMR][1000 genomes]
rs7520272	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7535826	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7541033	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549465	0.87[ASN][1000 genomes]
rs7549586	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7552783	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7555621	0.85[ASN][1000 genomes]
rs9726097	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9727512	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];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	nsv873237	chr1:227118912-227178948	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv873238	chr1:227118912-227180858	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv520923	chr1:227127618-227178948	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3768423	CDC42BPA	cis	Artery Tibial	GTEx
rs3768423	ADCK3	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227148600-227180800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
3	chr1:227158400-227183000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:227160800-227181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:227162400-227181600	Weak transcription	NHEK	skin
6	chr1:227163000-227180000	Weak transcription	HSMM	muscle
7	chr1:227163400-227191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:227163800-227180400	Weak transcription	Fetal Brain Male	brain
9	chr1:227170400-227177600	Strong transcription	Fetal Brain Female	brain
10	chr1:227170600-227177600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:227172600-227177600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:227173200-227177400	Enhancers	Brain Angular Gyrus	brain
13	chr1:227173200-227178200	Weak transcription	Fetal Kidney	kidney
14	chr1:227173400-227178200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:227173400-227178600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:227173400-227183400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:227173800-227177600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:227173800-227178400	Enhancers	Brain Cingulate Gyrus	brain
19	chr1:227174000-227178200	Enhancers	Brain Substantia Nigra	brain
20	chr1:227174800-227179400	Enhancers	Stomach Mucosa	stomach
21	chr1:227174800-227182000	Weak transcription	NHDF-Ad	bronchial
22	chr1:227175000-227178400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:227175200-227181200	Strong transcription	Fetal Muscle Leg	muscle
24	chr1:227175200-227198400	Weak transcription	A549	lung
25	chr1:227175200-227210200	Weak transcription	HMEC	breast
26	chr1:227175400-227178000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:227175400-227178400	Enhancers	Brain Hippocampus Middle	brain
28	chr1:227175400-227178400	Enhancers	Psoas Muscle	Psoas
29	chr1:227175400-227178800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr1:227175400-227182600	Genic enhancers	Fetal Intestine Small	intestine
31	chr1:227175600-227177400	Weak transcription	K562	blood
32	chr1:227175600-227178200	Enhancers	Duodenum Mucosa	Duodenum
33	chr1:227175600-227178200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr1:227175600-227178800	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr1:227175600-227179000	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr1:227175600-227179200	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr1:227175600-227180600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:227175600-227181600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:227175600-227182200	Weak transcription	Brain Germinal Matrix	brain
40	chr1:227175600-227183200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:227175600-227216200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:227175800-227177600	Weak transcription	Liver	Liver
43	chr1:227175800-227177800	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr1:227175800-227178000	Weak transcription	Ovary	ovary
45	chr1:227175800-227178400	Enhancers	Lung	lung
46	chr1:227175800-227178600	Enhancers	Colon Smooth Muscle	Colon
47	chr1:227175800-227179000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:227175800-227180400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:227175800-227181800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:227175800-227181800	Enhancers	Fetal Intestine Large	intestine

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