Variant report

Variant	rs5030707
Chromosome Location	chr20:23618656-23618657
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:264)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:264 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:23617945-23618771	GM19193	blood:	n/a	n/a
2	MXI1	chr20:23617859-23618827	HepG2	liver:	n/a	n/a
3	PAX5	chr20:23618176-23618753	GM12878	blood:	n/a	n/a
4	POLR2A	chr20:23618003-23618905	MCF-7	breast:	n/a	n/a
5	POLR2A	chr20:23618357-23618812	GM12878	blood:	n/a	n/a
6	REST	chr20:23618172-23618757	HepG2	liver:	n/a	n/a
7	POLR2A	chr20:23618335-23618692	K562	blood:	n/a	n/a
8	POLR2A	chr20:23617614-23618865	HUVEC	blood vessel:	n/a	n/a
9	MBD4	chr20:23618209-23618828	HepG2	liver:	n/a	n/a
10	MAZ	chr20:23617899-23618823	Hela-S3	cervix:	n/a	n/a
11	TAF1	chr20:23618162-23618833	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr20:23618110-23618849	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr20:23618038-23618783	PFSK-1	brain:	n/a	n/a
14	NR3C1	chr20:23618224-23618727	A549	lung:	n/a	n/a
15	POLR2A	chr20:23618242-23618846	A549	lung:	n/a	n/a
16	YY1	chr20:23618276-23618665	SK-N-SH_RA	brain:	n/a	chr20:23618531-23618542
17	POLR2A	chr20:23617842-23618715	Hela-S3	cervix:	n/a	n/a
18	GABPA	chr20:23618413-23618807	SK-N-SH	brain:	n/a	n/a
19	MAX	chr20:23617897-23618904	SK-N-SH	brain:	n/a	n/a
20	ZNF384	chr20:23618468-23618668	K562	blood:	n/a	n/a
21	POLR2A	chr20:23618325-23618817	SK-N-SH	brain:	n/a	n/a
22	CREB1	chr20:23617881-23618717	A549	lung:	n/a	n/a
23	POLR2A	chr20:23618325-23618825	HL-60	blood:	n/a	n/a
24	POLR2A	chr20:23618329-23618753	K562	blood:	n/a	n/a
25	RUNX3	chr20:23618307-23618717	GM12878	blood:	n/a	n/a
26	BHLHE40	chr20:23617931-23618730	HepG2	liver:	n/a	n/a
27	TCF7L2	chr20:23617937-23618758	HCT-116	colon:	n/a	n/a
28	SIN3AK20	chr20:23617724-23618913	MCF-7	breast:	n/a	n/a
29	TAF1	chr20:23618438-23618739	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr20:23618064-23618881	Gliobla	brain:	n/a	n/a
31	POLR2A	chr20:23617840-23618804	A549	lung:	n/a	n/a
32	ELF1	chr20:23618251-23618831	HepG2	liver:	n/a	n/a
33	MYC	chr20:23618304-23618735	HepG2	liver:	n/a	n/a
34	STAT1	chr20:23618444-23618695	GM12878	blood:	n/a	n/a
35	POLR2A	chr20:23617922-23618752	Hela-S3	cervix:	n/a	n/a
36	SIN3AK20	chr20:23618385-23618691	SK-N-SH	brain:	n/a	n/a
37	PML	chr20:23618236-23618759	MCF-7	breast:	n/a	n/a
38	RFX5	chr20:23618457-23618735	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr20:23614494-23618787	HepG2	liver:	n/a	n/a
40	RFX5	chr20:23617948-23618682	HepG2	liver:	n/a	n/a
41	POLR2A	chr20:23618125-23618753	GM12878	blood:	n/a	n/a
42	E2F4	chr20:23618550-23618769	MCF10A-Er-Src	breast:	n/a	n/a
43	MAX	chr20:23617801-23618892	MCF-7	breast:	n/a	n/a
44	POLR2A	chr20:23617882-23618711	A549	lung:	n/a	n/a
45	MAX	chr20:23617646-23618929	A549	lung:	n/a	n/a
46	GABPA	chr20:23618296-23618778	A549	lung:	n/a	n/a
47	ELF1	chr20:23617824-23618891	GM12878	blood:	n/a	chr20:23618216-23618228
48	POLR2A	chr20:23611829-23619325	HepG2	liver:	n/a	n/a
49	IRF1	chr20:23618484-23618821	K562	blood:	n/a	n/a
50	NR3C1	chr20:23618404-23618805	A549	lung:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:23617167..23619413-chr20:62495612..62498216,2	MCF-7	breast:
2	chr20:23340884..23343229-chr20:23616953..23618725,2	K562	blood:
3	chr20:23400787..23402892-chr20:23617355..23620191,2	MCF-7	breast:
4	chr20:23400310..23402508-chr20:23615661..23618868,3	MCF-7	breast:
5	chr20:23608610..23615599-chr20:23616056..23619619,19	MCF-7	breast:
6	chr20:23618414..23619171-chr5:138940732..138941254,2	HCT-116	colon:
7	chr20:23342009..23344759-chr20:23616093..23619702,3	MCF-7	breast:
8	chr15:93425841..93426770-chr20:23617945..23618689,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
CST3	TF binding region
ENSG00000272888	Chromatin interaction
ENSG00000131508	Chromatin interaction
ENSG00000101150	Chromatin interaction
ENSG00000270001	Chromatin interaction
ENSG00000125812	Chromatin interaction
ENSG00000173575	Chromatin interaction
ENSG00000125814	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1010117	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1011226	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1064039	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12624424	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12625182	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12625716	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13037490	0.82[EUR][1000 genomes]
rs13038305	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13038337	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13038990	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13039536	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13041070	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13043266	0.85[EUR][1000 genomes]
rs13043610	0.84[EUR][1000 genomes]
rs1555355	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17751897	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2016161	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067488	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2254635	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2405367	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2424582	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703706	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2897119	0.83[EUR][1000 genomes]
rs3088162	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34374560	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34746357	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34792920	0.81[EUR][1000 genomes]
rs34897231	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34911568	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35488434	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35573837	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35610040	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35782710	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35966482	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761280	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761281	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787498	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787499	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827141	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3827142	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827143	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815224	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55897275	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56371840	0.84[EUR][1000 genomes]
rs56388902	0.83[EUR][1000 genomes]
rs57549987	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59059917	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036465	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6036469	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6036470	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036471	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6036474	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6036476	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6036478	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6048923	0.82[EUR][1000 genomes]
rs6048928	0.84[EUR][1000 genomes]
rs6048929	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048933	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048936	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048941	0.81[EUR][1000 genomes]
rs6048945	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048946	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048949	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048950	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048952	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048956	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61035931	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6114201	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6114206	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6114208	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114209	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6515375	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67567111	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67997662	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71334202	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7265178	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7270413	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73318135	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734801	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8114619	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8115417	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8115423	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8116859	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8121147	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8121283	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8121405	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs911119	0.93[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	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv964381	chr20:23614805-23621846	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	esv3359195	chr20:23617352-23620750	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	esv3377051	chr20:23617777-23620325	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3336303	chr20:23617902-23620300	Weak transcription Active TSS Enhancers Flanking 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	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5030707	CST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23617200-23618800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr20:23617200-23618800	Active TSS	Brain Cingulate Gyrus	brain
3	chr20:23617400-23618800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr20:23617400-23618800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr20:23617400-23618800	Active TSS	Psoas Muscle	Psoas
6	chr20:23617400-23618800	Active TSS	Right Atrium	heart
7	chr20:23617400-23618800	Active TSS	Right Ventricle	heart
8	chr20:23617600-23618800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr20:23617600-23618800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr20:23617600-23618800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr20:23617600-23618800	Active TSS	Primary B cells from cord blood	blood
12	chr20:23617600-23618800	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr20:23617600-23618800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr20:23617600-23618800	Active TSS	Colonic Mucosa	Colon
15	chr20:23617600-23618800	Active TSS	Fetal Intestine Large	intestine
16	chr20:23617600-23618800	Active TSS	Lung	lung
17	chr20:23617600-23618800	Active TSS	Pancreas	Pancrea
18	chr20:23617600-23618800	Active TSS	Hela-S3	cervix
19	chr20:23617600-23618800	Active TSS	NHEK	skin
20	chr20:23617600-23619200	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr20:23617600-23619200	Active TSS	Fetal Brain Female	brain
22	chr20:23617800-23618800	Active TSS	H1 Cell Line	embryonic stem cell
23	chr20:23617800-23618800	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr20:23617800-23618800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr20:23617800-23618800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr20:23617800-23618800	Active TSS	Primary monocytes fromperipheralblood	blood
27	chr20:23617800-23618800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr20:23617800-23618800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr20:23617800-23618800	Active TSS	Adipose Nuclei	Adipose
30	chr20:23617800-23618800	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr20:23617800-23618800	Active TSS	Fetal Stomach	stomach
32	chr20:23617800-23618800	Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr20:23617800-23618800	Active TSS	Stomach Smooth Muscle	stomach
34	chr20:23617800-23618800	Active TSS	A549	lung
35	chr20:23617800-23618800	Active TSS	HSMM	muscle
36	chr20:23617800-23618800	Active TSS	HSMMtube	muscle
37	chr20:23617800-23618800	Active TSS	Monocytes-CD14+_RO01746	blood
38	chr20:23617800-23618800	Active TSS	NH-A	brain
39	chr20:23617800-23618800	Active TSS	Osteobl	bone
40	chr20:23617800-23619000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr20:23617800-23619200	Active TSS	H9 Cell Line	embryonic stem cell
42	chr20:23617800-23619200	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr20:23617800-23619200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr20:23618000-23618800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr20:23618000-23618800	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr20:23618000-23618800	Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr20:23618000-23618800	Active TSS	Brain Germinal Matrix	brain
48	chr20:23618000-23618800	Active TSS	Fetal Lung	lung
49	chr20:23618000-23618800	Active TSS	Fetal Muscle Leg	muscle
50	chr20:23618000-23618800	Active TSS	Placenta	Placenta

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