Variant report

Variant	rs74140289
Chromosome Location	chr1:227272809-227272810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:227272582-227272882	K562	blood:	n/a	n/a

Variant related genes	Relation type
CDC42BPA	TF binding region

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10495266	0.81[AFR][1000 genomes]
rs11799413	0.81[AFR][1000 genomes]
rs11801443	0.81[AFR][1000 genomes]
rs11802395	0.81[AFR][1000 genomes]
rs11803919	0.85[AFR][1000 genomes]
rs11803959	0.81[AFR][1000 genomes]
rs11806820	0.81[AFR][1000 genomes]
rs11807094	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11808186	0.81[AFR][1000 genomes]
rs11808962	1.00[AMR][1000 genomes]
rs11811100	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12401963	0.81[AFR][1000 genomes]
rs12403391	0.83[AFR][1000 genomes]
rs12404494	0.83[AFR][1000 genomes]
rs12405122	0.81[AFR][1000 genomes]
rs12405686	0.81[AFR][1000 genomes]
rs12405878	0.81[AFR][1000 genomes]
rs12407545	0.81[AFR][1000 genomes]
rs12408437	0.81[AFR][1000 genomes]
rs12410337	0.81[AFR][1000 genomes]
rs12410460	0.81[AFR][1000 genomes]
rs12411017	0.81[AFR][1000 genomes]
rs1320493	0.81[AFR][1000 genomes]
rs1513600	0.83[AFR][1000 genomes]
rs16846855	0.81[AFR][1000 genomes]
rs16846874	0.81[AFR][1000 genomes]
rs16846908	0.81[AFR][1000 genomes]
rs16846910	0.81[AFR][1000 genomes]
rs16846911	0.81[AFR][1000 genomes]
rs16846985	0.81[AFR][1000 genomes]
rs16847014	0.81[AFR][1000 genomes]
rs16847035	0.81[AFR][1000 genomes]
rs16847098	0.81[AFR][1000 genomes]
rs16847249	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17851754	0.81[AFR][1000 genomes]
rs1888830	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1888831	0.81[AFR][1000 genomes]
rs2090009	0.81[AFR][1000 genomes]
rs2150871	0.81[AFR][1000 genomes]
rs2150873	0.81[AFR][1000 genomes]
rs2183837	0.81[AFR][1000 genomes]
rs55685166	0.81[AFR][1000 genomes]
rs55865118	0.81[AFR][1000 genomes]
rs56352806	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57454791	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57513303	0.81[AFR][1000 genomes]
rs57752854	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58532064	0.81[AFR][1000 genomes]
rs58594824	0.87[AMR][1000 genomes]
rs58912997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59136460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60291100	0.81[AFR][1000 genomes]
rs60483746	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60979561	0.81[AFR][1000 genomes]
rs6696794	0.81[AFR][1000 genomes]
rs6701743	0.83[AFR][1000 genomes]
rs73089725	0.83[AFR][1000 genomes]
rs73089746	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089747	0.83[AFR][1000 genomes]
rs73089755	0.81[AFR][1000 genomes]
rs73089760	0.81[AFR][1000 genomes]
rs73089765	0.81[AFR][1000 genomes]
rs73089770	0.81[AFR][1000 genomes]
rs73091738	0.81[AFR][1000 genomes]
rs73091740	0.81[AFR][1000 genomes]
rs73091742	0.81[AFR][1000 genomes]
rs73091757	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091761	0.81[AFR][1000 genomes]
rs73091766	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091774	0.81[AFR][1000 genomes]
rs73092520	1.00[AMR][1000 genomes]
rs73092602	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093463	0.81[AFR][1000 genomes]
rs73093467	0.97[AFR][1000 genomes]
rs73093495	0.83[AFR][1000 genomes]
rs73094331	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094355	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73096883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73099023	0.81[AFR][1000 genomes]
rs73099026	0.81[AFR][1000 genomes]
rs73100804	0.81[AFR][1000 genomes]
rs73100813	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73100814	0.80[AFR][1000 genomes]
rs73102918	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74140233	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs74140276	0.81[AFR][1000 genomes]
rs74140278	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7525352	1.00[AMR][1000 genomes];1.00[EUR][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	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv468227	chr1:227223736-227340790	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv549269	chr1:227223736-227340790	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv998420	chr1:227228591-227275031	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	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
10	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

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227203000-227278800	Weak transcription	Pancreas	Pancrea
3	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
5	chr1:227216800-227287600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:227217000-227278800	Weak transcription	Placenta	Placenta
7	chr1:227220600-227288000	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:227226800-227278400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:227226800-227285600	Weak transcription	Brain Germinal Matrix	brain
10	chr1:227227000-227282200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:227227400-227281200	Weak transcription	Fetal Kidney	kidney
12	chr1:227227400-227284200	Weak transcription	Brain Angular Gyrus	brain
13	chr1:227228000-227277000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:227232800-227279200	Weak transcription	Stomach Mucosa	stomach
15	chr1:227236000-227286200	Weak transcription	Fetal Brain Male	brain
16	chr1:227238600-227278400	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:227240000-227286800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:227246400-227278400	Weak transcription	NH-A	brain
19	chr1:227247400-227299800	Weak transcription	HMEC	breast
20	chr1:227251000-227300000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:227253600-227278600	Weak transcription	Adipose Nuclei	Adipose
22	chr1:227257000-227278400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:227257600-227288000	Weak transcription	HSMMtube	muscle
24	chr1:227257800-227312200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:227259000-227280600	Weak transcription	HepG2	liver
26	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
27	chr1:227260000-227278600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:227260200-227278600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:227260200-227281800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:227260400-227287800	Weak transcription	NHEK	skin
31	chr1:227261000-227274400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:227261400-227287800	Weak transcription	Osteobl	bone
33	chr1:227268600-227278600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:227268800-227287000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:227270200-227278400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:227270400-227275000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:227270600-227273000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:227270800-227273000	Strong transcription	HUVEC	blood vessel
39	chr1:227270800-227275800	Strong transcription	HSMM	muscle
40	chr1:227270800-227276000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:227271200-227273000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
42	chr1:227271200-227273000	Strong transcription	K562	blood
43	chr1:227271400-227273000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:227271400-227273000	Strong transcription	Fetal Intestine Large	intestine
45	chr1:227271400-227274200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
46	chr1:227271400-227276000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:227271800-227273000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:227271800-227273000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:227271800-227273800	Strong transcription	Fetal Muscle Trunk	muscle
50	chr1:227271800-227274000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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