Variant report

Variant	rs2239516
Chromosome Location	chr6:30578048-30578049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:70)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:70 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30576348-30586731	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr6:30577459-30579248	HCT-116	colon:	n/a	n/a
3	POLR2A	chr6:30576760-30578592	A549	lung:	n/a	n/a
4	NFATC1	chr6:30577523-30578608	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:30577264-30578758	U87	brain:	n/a	n/a
6	POLR2A	chr6:30576459-30586534	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr6:30577620-30578176	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr6:30576762-30586531	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr6:30576975-30579686	K562	blood:	n/a	n/a
10	POLR2A	chr6:30576843-30586279	HCT-116	colon:	n/a	n/a
11	POLR2A	chr6:30577898-30578617	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr6:30577732-30579148	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:30576894-30586563	PANC-1	pancreas:	n/a	n/a
14	USF2	chr6:30577911-30578105	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr6:30577518-30578619	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:30577680-30578598	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:30576267-30586793	SK-N-MC	brain:	n/a	n/a
18	NFATC1	chr6:30577691-30578686	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:30576421-30586088	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr6:30577892-30578126	GM12891	blood:	n/a	n/a
21	POLR2A	chr6:30576151-30586136	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr6:30576533-30586585	GM12891	blood:	n/a	n/a
23	POLR2A	chr6:30577091-30578663	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr6:30577424-30578552	GM18505	blood:	n/a	n/a
25	HEY1	chr6:30577465-30578874	HepG2	liver:	n/a	n/a
26	POLR2A	chr6:30577530-30579223	K562	blood:	n/a	n/a
27	POLR2A	chr6:30576971-30585965	U87	brain:	n/a	n/a
28	POLR2A	chr6:30577744-30578185	Raji	blood:	n/a	n/a
29	POLR2A	chr6:30576897-30586493	K562	blood:	n/a	n/a
30	POLR2A	chr6:30577627-30578589	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:30576601-30586578	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:30577488-30586361	PBDE	blood:	n/a	n/a
33	POLR2A	chr6:30576348-30586293	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr6:30577512-30578646	K562	blood:	n/a	n/a
35	POLR2A	chr6:30577185-30578687	SK-N-MC	brain:	n/a	n/a
36	MTA3	chr6:30577400-30578549	GM12878	blood:	n/a	n/a
37	POLR2A	chr6:30577909-30578698	HEK293	kidney:	n/a	n/a
38	POLR2A	chr6:30577342-30579349	HepG2	liver:	n/a	n/a
39	POLR2A	chr6:30577808-30578183	HepG2	liver:	n/a	n/a
40	POLR2A	chr6:30577264-30579275	U87	brain:	n/a	n/a
41	POLR2A	chr6:30577732-30578190	GM12891	blood:	n/a	n/a
42	POLR2A	chr6:30577776-30579117	K562	blood:	n/a	n/a
43	POLR2A	chr6:30576539-30586508	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr6:30576353-30586641	PFSK-1	brain:	n/a	n/a
45	POLR2A	chr6:30577075-30578768	K562	blood:	n/a	n/a
46	POLR2A	chr6:30577896-30578088	GM12878	blood:	n/a	n/a
47	POLR2A	chr6:30577852-30578112	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr6:30577518-30578207	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr6:30576529-30586246	MCF-7	breast:	n/a	n/a
50	POLR2A	chr6:30576649-30578604	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30577773..30589670-chr6:30680333..30700280,58	MCF-7	breast:
2	chr6:30577862..30587208-chr6:30682997..30696247,43	MCF-7	breast:
3	chr6:30577127..30589352-chr6:30620628..30648657,88	K562	blood:
4	chr6:30452366..30463564-chr6:30577885..30586736,19	MCF-7	breast:
5	chr6:30511109..30514018-chr6:30576685..30580337,3	MCF-7	breast:
6	chr6:30520810..30527475-chr6:30577152..30588201,32	MCF-7	breast:
7	chr19:54710768..54711555-chr6:30577873..30578659,2	HCT-116	colon:
8	chr6:30577364..30581812-chr6:30612731..30615596,7	MCF-7	breast:
9	chr6:30576975..30585099-chr6:30622978..30628754,9	MCF-7	breast:
10	chr6:30501371..30504136-chr6:30577423..30580435,3	K562	blood:
11	chr6:30576582..30588788-chr6:30682721..30700088,114	K562	blood:
12	chr6:30517868..30527565-chr6:30576812..30587078,24	MCF-7	breast:

No data

Variant related genes	Relation type
PPP1R10	TF binding region
ENSG00000204592	Chromatin interaction
ENSG00000236603	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000204564	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000204560	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs16867845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189120	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189155	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17195411	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17195474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17195488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17195516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17195544	0.86[AFR][1000 genomes]
rs2106069	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270172	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2302347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394387	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394388	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2394389	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3815101	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3888777	0.83[AMR][1000 genomes]
rs4148247	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57626358	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs58423891	0.94[ASN][1000 genomes]
rs59272830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59607822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59913575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60081418	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60365864	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs60399658	0.88[ASN][1000 genomes]
rs61733213	0.88[ASN][1000 genomes]
rs6457246	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899769	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899862	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6901251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911174	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917434	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917935	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927727	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6934466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742754	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749109	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749807	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7749978	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773711	0.88[ASN][1000 genomes]
rs9262120	1.00[ASN][1000 genomes]
rs9468812	0.88[ASN][1000 genomes]
rs9468821	0.82[ASN][1000 genomes]
rs9468822	0.82[ASN][1000 genomes]
rs9468823	0.82[ASN][1000 genomes]
rs9500865	0.82[ASN][1000 genomes]
rs9671	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS 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	1012 gene(s)	inside rSNPs	diseases
5	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
7	nsv884091	chr6:30526026-30590646	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	776 gene(s)	inside rSNPs	diseases
8	nsv5244	chr6:30545111-30589803	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers 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	772 gene(s)	inside rSNPs	diseases
9	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2239516	ABCF1	cis	multi-tissue	Pritchard
rs2239516	ARC	trans	brain	seeQTL
rs2239516	MRPS18B	cis	lymphoblastoid	seeQTL
rs2239516	NPAS4	trans	brain	seeQTL
rs2239516	INHBA	trans	brain	seeQTL
rs2239516	PRR3	cis	lymphoblastoid	seeQTL
rs2239516	SERTAD1	trans	brain	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30540200-30582200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:30540200-30582200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:30542200-30581800	Weak transcription	Right Atrium	heart
4	chr6:30566400-30581000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:30566600-30579600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:30566800-30578400	Strong transcription	Thymus	Thymus
7	chr6:30567000-30579400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:30567000-30579600	Strong transcription	Fetal Muscle Trunk	muscle
9	chr6:30567200-30579600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:30567400-30578200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:30567400-30578200	Strong transcription	Fetal Muscle Leg	muscle
12	chr6:30567400-30579000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:30567400-30579200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:30567400-30579800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:30567400-30580000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:30567400-30580200	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:30567400-30580400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:30567600-30578400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:30567600-30580400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:30568000-30578200	Strong transcription	Dnd41	blood
21	chr6:30568000-30580000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:30568000-30580200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:30568200-30579200	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr6:30568200-30579600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr6:30568200-30579800	Strong transcription	A549	lung
26	chr6:30568200-30579800	Strong transcription	NHEK	skin
27	chr6:30568400-30578200	Strong transcription	Liver	Liver
28	chr6:30568400-30578200	Strong transcription	NHLF	lung
29	chr6:30568400-30578400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
30	chr6:30568400-30578400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:30568400-30579000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:30568400-30579600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:30568400-30580000	Strong transcription	K562	blood
34	chr6:30568400-30580800	Strong transcription	GM12878-XiMat	blood
35	chr6:30568600-30578200	Strong transcription	HepG2	liver
36	chr6:30568800-30579000	Strong transcription	HUVEC	blood vessel
37	chr6:30570200-30578200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:30570200-30579000	Strong transcription	Fetal Thymus	thymus
39	chr6:30570200-30579200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:30570600-30579200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:30570800-30578400	Strong transcription	NHDF-Ad	bronchial
42	chr6:30574600-30578800	Weak transcription	Psoas Muscle	Psoas
43	chr6:30574600-30582200	Weak transcription	Small Intestine	intestine
44	chr6:30574600-30582400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:30575400-30578400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr6:30575600-30579400	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr6:30576200-30579400	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr6:30576400-30581600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr6:30576800-30579600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:30577000-30578200	Genic enhancers	Primary T helper cells fromperipheralblood	blood

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