Variant report

Variant	rs6724
Chromosome Location	chr1:153932212-153932213
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:153930247-153932267	K562	blood:	n/a	n/a
2	POLR2A	chr1:153929336-153932363	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:153929724-153932525	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:153932134-153932433	A549	lung:	n/a	n/a
5	POLR2A	chr1:153932111-153932277	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:153929838-153932756	PFSK-1	brain:	n/a	n/a
7	HCFC1	chr1:153929780-153932740	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:153931946-153932375	HepG2	liver:	n/a	n/a
9	SP1	chr1:153931542-153932480	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:153929691-153932392	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr1:153930121-153932796	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr1:153932179-153932220	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr1:153931897-153932414	K562	blood:	n/a	n/a
14	POLR2A	chr1:153931982-153932373	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153793084..153795411-chr1:153931353..153934057,2	MCF-7	breast:
2	chr1:153635410..153637927-chr1:153928123..153932423,3	K562	blood:
3	chr1:153747107..153752136-chr1:153929206..153936862,9	MCF-7	breast:

No data

Variant related genes	Relation type
CRTC2	TF binding region
ENSG00000143621	Chromatin interaction
ENSG00000143554	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10127983	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1043608	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10559	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10796968	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10908557	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908558	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1110165	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264532	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264559	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264567	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11264619	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264620	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264680	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264734	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264743	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264763	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11577942	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11581644	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11583152	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11585416	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11586075	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11586593	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11586830	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11587151	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11589043	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11589857	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11590099	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11591134	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12022158	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12022730	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12023699	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12027783	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12028398	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12032914	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12033835	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12038577	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12041850	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12041920	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12042562	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12042989	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12043350	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12401565	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12403956	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12406003	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12409811	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12567313	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1547766	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1547767	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1572788	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34805562	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3748848	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748849	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3791187	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508047	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4520447	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4595397	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4612664	0.84[ASN][1000 genomes]
rs4845357	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845358	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845576	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4845578	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4845583	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845585	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58095661	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59308681	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59678326	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60150125	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61219911	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427329	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6659220	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6666703	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671132	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6680140	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6694061	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6700451	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72694231	0.81[ASN][1000 genomes]
rs72694234	0.84[ASN][1000 genomes]
rs7524739	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7537691	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7552274	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8450	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs946682	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9660089	0.82[EUR][1000 genomes];0.84[ASN][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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv872450	chr1:153889042-153937513	Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	nsv532552	chr1:153912047-153950752	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153931000-153935800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:153931200-153932400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:153931200-153932400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:153931200-153932400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:153931200-153932600	Weak transcription	Aorta	Aorta
6	chr1:153931200-153932600	Enhancers	Fetal Heart	heart
7	chr1:153931200-153932600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:153931200-153932800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:153931200-153932800	Weak transcription	Esophagus	oesophagus
10	chr1:153931200-153934000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:153931200-153934000	Weak transcription	HSMMtube	muscle
12	chr1:153931400-153933400	Enhancers	Right Atrium	heart
13	chr1:153931400-153933800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:153931400-153934000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:153931400-153934200	Weak transcription	Small Intestine	intestine
16	chr1:153931400-153934400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:153931600-153932400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:153931600-153932400	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:153931600-153932400	Enhancers	Pancreas	Pancrea
20	chr1:153931600-153932400	Enhancers	Right Ventricle	heart
21	chr1:153931600-153932600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:153931600-153932600	Weak transcription	Brain Anterior Caudate	brain
23	chr1:153931600-153932600	Genic enhancers	K562	blood
24	chr1:153931600-153932800	Genic enhancers	Liver	Liver
25	chr1:153931600-153932800	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr1:153931600-153933000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:153931600-153933000	Genic enhancers	Fetal Stomach	stomach
28	chr1:153931600-153933200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:153931600-153933200	Weak transcription	Osteobl	bone
30	chr1:153931600-153933400	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr1:153931600-153933800	Genic enhancers	Placenta	Placenta
32	chr1:153931600-153934000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:153931600-153934000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:153931600-153934000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr1:153931600-153934000	Weak transcription	Stomach Mucosa	stomach
36	chr1:153931600-153934000	Weak transcription	HUVEC	blood vessel
37	chr1:153931600-153934000	Weak transcription	NH-A	brain
38	chr1:153931600-153934200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:153931600-153934200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:153931600-153934200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr1:153931600-153934400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:153931600-153934400	Weak transcription	HSMM	muscle
43	chr1:153931600-153934600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr1:153931600-153934600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:153931600-153934600	Genic enhancers	Fetal Muscle Leg	muscle
46	chr1:153931600-153934600	Enhancers	Psoas Muscle	Psoas
47	chr1:153931800-153932400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:153931800-153932400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:153931800-153932400	Enhancers	Rectal Smooth Muscle	rectum
50	chr1:153931800-153932600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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