Variant report

Variant	rs6426558
Chromosome Location	chr1:227175367-227175368
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:227173495-227175725	K562	blood:	n/a	n/a
2	POLR2A	chr1:227171755-227176557	K562	blood:	n/a	n/a
3	POLR2A	chr1:227174808-227176568	HL-60	blood:	n/a	n/a
4	POLR2A	chr1:227170173-227176506	K562	blood:	n/a	n/a
5	FOSL2	chr1:227175253-227176471	HepG2	liver:	n/a	chr1:227176439-227176451
6	POLR2A	chr1:227174968-227176363	HL-60	blood:	n/a	n/a
7	POLR2A	chr1:227172012-227175716	K562	blood:	n/a	n/a
8	POLR2A	chr1:227169948-227179599	K562	blood:	n/a	n/a
9	POLR2A	chr1:227170107-227176585	K562	blood:	n/a	n/a
10	POLR2A	chr1:227175232-227175600	K562	blood:	n/a	n/a
11	POLR2A	chr1:227174148-227176843	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227166708..227168288-chr1:227175078..227176909,2	MCF-7	breast:
2	chr1:227165601..227167978-chr1:227173311..227176266,3	MCF-7	breast:
3	chr1:227154071..227157064-chr1:227173659..227175478,2	MCF-7	breast:
4	chr1:227128683..227130385-chr1:227174300..227176049,2	MCF-7	breast:
5	chr1:227173653..227176046-chr1:227186826..227189560,2	MCF-7	breast:
6	chr1:227173983..227176329-chr1:227192052..227193578,2	MCF-7	breast:
7	chr1:227126152..227130822-chr1:227174735..227178540,5	MCF-7	breast:
8	chr1:227168074..227172579-chr1:227173053..227177156,6	MCF-7	breast:
9	chr1:227100125..227100781-chr1:227175209..227175979,2	MCF-7	breast:

No data

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

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1045252	1.00[CHB][hapmap]
rs1045285	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1045286	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1045287	0.88[AMR][1000 genomes]
rs1045289	0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1045290	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10495273	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10916075	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11577007	0.88[AMR][1000 genomes]
rs11578103	0.87[AMR][1000 genomes]
rs11578479	0.81[AMR][1000 genomes]
rs11580229	0.81[AMR][1000 genomes]
rs11586604	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11587443	1.00[CHB][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11588904	0.86[AMR][1000 genomes]
rs11589344	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1186	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12403236	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12406714	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12409230	0.86[AMR][1000 genomes]
rs12409428	0.88[AMR][1000 genomes]
rs12409755	0.87[AMR][1000 genomes]
rs12410103	0.86[AMR][1000 genomes]
rs12593	0.81[AMR][1000 genomes]
rs1343743	0.87[AMR][1000 genomes]
rs1343744	0.85[AMR][1000 genomes]
rs17528667	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17592479	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17600627	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17600669	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17600725	0.81[AMR][1000 genomes]
rs1929862	1.00[CHB][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1929863	0.87[AMR][1000 genomes]
rs1929864	0.87[AMR][1000 genomes]
rs2183836	0.90[CHB][hapmap];0.96[ASN][1000 genomes]
rs2297412	0.83[ASN][1000 genomes]
rs2297415	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2297416	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2297418	0.87[AMR][1000 genomes]
rs3738725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738729	0.86[AMR][1000 genomes]
rs3768419	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3768421	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3768423	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3768424	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768425	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3795445	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3795446	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3795449	0.88[AMR][1000 genomes]
rs3795451	0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3795453	0.81[AMR][1000 genomes]
rs61834001	0.87[AMR][1000 genomes]
rs61834004	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61834005	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61834006	0.83[AMR][1000 genomes]
rs6426559	0.87[AMR][1000 genomes]
rs6659424	0.86[AMR][1000 genomes]
rs6664955	0.88[AMR][1000 genomes]
rs6670924	0.87[AMR][1000 genomes]
rs6684821	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6690803	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6693535	0.87[AMR][1000 genomes]
rs6699400	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6704144	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs68087483	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7520272	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7535826	0.81[AMR][1000 genomes]
rs7541033	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7549586	0.83[AMR][1000 genomes]
rs7552783	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9726097	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9727512	0.81[AFR][1000 genomes];0.88[AMR][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
rs6426558	ADCK3	cis	Whole Blood	GTEx
rs6426558	CDC42BPA	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227147000-227177000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:227148600-227180800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
4	chr1:227154800-227176800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:227158400-227183000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:227159000-227175800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:227160000-227177200	Weak transcription	GM12878-XiMat	blood
8	chr1:227160600-227175600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:227160800-227181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:227162200-227176000	Strong transcription	Primary T cells from cord blood	blood
11	chr1:227162400-227181600	Weak transcription	NHEK	skin
12	chr1:227162600-227175800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:227162600-227176600	Strong transcription	Thymus	Thymus
14	chr1:227163000-227180000	Weak transcription	HSMM	muscle
15	chr1:227163200-227175400	Strong transcription	Fetal Intestine Small	intestine
16	chr1:227163400-227191200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:227163800-227176200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:227163800-227180400	Weak transcription	Fetal Brain Male	brain
19	chr1:227164200-227175800	Strong transcription	HepG2	liver
20	chr1:227164400-227175600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:227165000-227175400	Genic enhancers	Right Ventricle	heart
22	chr1:227165000-227176000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr1:227165400-227175800	Strong transcription	Ovary	ovary
24	chr1:227168800-227175400	Weak transcription	Psoas Muscle	Psoas
25	chr1:227168800-227175600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:227168800-227175600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
27	chr1:227169200-227175400	Strong transcription	Fetal Thymus	thymus
28	chr1:227169600-227175800	Strong transcription	Liver	Liver
29	chr1:227169800-227175800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:227170000-227176000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:227170200-227175400	Strong transcription	Colon Smooth Muscle	Colon
32	chr1:227170400-227176200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:227170400-227176400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr1:227170400-227177600	Strong transcription	Fetal Brain Female	brain
35	chr1:227170600-227177600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:227170800-227176200	Genic enhancers	Left Ventricle	heart
37	chr1:227171200-227175400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:227171400-227175600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:227172000-227175600	Strong transcription	Primary B cells from cord blood	blood
40	chr1:227172000-227175600	Strong transcription	Brain Germinal Matrix	brain
41	chr1:227172200-227175400	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr1:227172200-227175600	Genic enhancers	Pancreas	Pancrea
43	chr1:227172400-227175400	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr1:227172600-227177600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr1:227172800-227176200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:227172800-227176200	Genic enhancers	Spleen	Spleen
47	chr1:227172800-227176600	Weak transcription	HSMMtube	muscle
48	chr1:227173000-227175400	Genic enhancers	Brain Hippocampus Middle	brain
49	chr1:227173000-227176000	Strong transcription	Fetal Stomach	stomach
50	chr1:227173200-227177400	Enhancers	Brain Angular Gyrus	brain

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