Variant report

Variant	rs3752848
Chromosome Location	chr6:117923599-117923600
allele	A/G
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	chr6:117923035-117924273	NB4	blood:	n/a	n/a
2	MAZ	chr6:117923182-117924097	GM12878	blood:	n/a	n/a
3	CHD2	chr6:117922947-117924094	K562	blood:	n/a	chr6:117923954-117923964 chr6:117923569-117923579
4	RAD21	chr6:117922474-117923848	IMR90	lung:	n/a	chr6:117923113-117923126 chr6:117923490-117923502
5	YY1	chr6:117923255-117924107	GM12892	blood:	n/a	chr6:117923535-117923549 chr6:117923805-117923815 chr6:117923804-117923816 chr6:117923490-117923499 chr6:117923683-117923697 chr6:117923805-117923827
6	POLR2A	chr6:117923017-117924659	MCF-7	breast:	n/a	n/a
7	SIN3AK20	chr6:117923167-117923979	HepG2	liver:	n/a	n/a
8	BRCA1	chr6:117923592-117924110	Hela-S3	cervix:	n/a	n/a
9	USF2	chr6:117923567-117924068	HepG2	liver:	n/a	n/a
10	ZNF143	chr6:117922576-117924200	K562	blood:	n/a	chr6:117923674-117923693 chr6:117923684-117923694
11	YY1	chr6:117922856-117924238	GM12878	blood:	n/a	chr6:117923535-117923549 chr6:117923805-117923815 chr6:117923804-117923816 chr6:117923490-117923499 chr6:117923683-117923697 chr6:117923805-117923827
12	TAF1	chr6:117923150-117924220	A549	lung:	n/a	n/a
13	MYC	chr6:117923407-117924186	MCF-7	breast:	n/a	n/a
14	IRF1	chr6:117923259-117924234	K562	blood:	n/a	chr6:117923742-117923756
15	ZBTB7A	chr6:117923252-117923678	HepG2	liver:	n/a	n/a
16	HMGN3	chr6:117923170-117924054	K562	blood:	n/a	n/a
17	POU2F2	chr6:117923326-117924001	GM12891	blood:	n/a	n/a
18	POLR2A	chr6:117923348-117924444	GM12878	blood:	n/a	n/a
19	HCFC1	chr6:117922825-117924670	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr6:117922828-117924695	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr6:117923150-117924547	U87	brain:	n/a	n/a
22	MAX	chr6:117922912-117924212	HepG2	liver:	n/a	chr6:117923007-117923017
23	RUNX3	chr6:117922844-117924300	GM12878	blood:	n/a	n/a
24	ZNF143	chr6:117923263-117924190	GM12878	blood:	n/a	chr6:117923674-117923693 chr6:117923684-117923694
25	MYC	chr6:117923489-117923843	MCF-7	breast:	n/a	n/a
26	EP300	chr6:117923572-117924245	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:117923412-117923948	A549	lung:	n/a	n/a
28	MYC	chr6:117923374-117924089	MCF-7	breast:	n/a	n/a
29	HCFC1	chr6:117922978-117924242	K562	blood:	n/a	n/a
30	MAX	chr6:117922659-117924531	HepG2	liver:	n/a	chr6:117923007-117923017
31	PAX5	chr6:117923245-117923820	GM12892	blood:	n/a	chr6:117923540-117923549
32	POLR2A	chr6:117922916-117924429	K562	blood:	n/a	n/a
33	POLR2A	chr6:117923411-117924279	GM12891	blood:	n/a	n/a
34	SP1	chr6:117923505-117924072	H1-hESC	embryonic stem cell:	n/a	chr6:117923742-117923753 chr6:117923670-117923684
35	E2F6	chr6:117923328-117924185	H1-hESC	embryonic stem cell:	n/a	chr6:117923696-117923705 chr6:117923684-117923694
36	GTF2F1	chr6:117923124-117923990	K562	blood:	n/a	n/a
37	TBP	chr6:117922919-117924236	HepG2	liver:	n/a	n/a
38	MAX	chr6:117922957-117924447	HCT-116	colon:	n/a	chr6:117923007-117923017
39	GABPA	chr6:117923476-117924139	A549	lung:	n/a	chr6:117924037-117924048 chr6:117923695-117923706 chr6:117923536-117923545 chr6:117923692-117923706 chr6:117923534-117923543 chr6:117924037-117924051 chr6:117924034-117924048 chr6:117923695-117923704 chr6:117923538-117923547 chr6:117923695-117923709
40	YY1	chr6:117922848-117924189	K562	blood:	n/a	chr6:117923535-117923549 chr6:117923805-117923815 chr6:117923804-117923816 chr6:117923490-117923499 chr6:117923683-117923697 chr6:117923805-117923827
41	TCF3	chr6:117923306-117923728	GM12878	blood:	n/a	n/a
42	RELA	chr6:117923170-117924311	GM15510	blood:	n/a	n/a
43	TAF1	chr6:117923482-117923960	PFSK-1	brain:	n/a	n/a
44	WRNIP1	chr6:117922902-117924430	GM12878	blood:	n/a	n/a
45	POLR2A	chr6:117923404-117923944	A549	lung:	n/a	n/a
46	PAX5	chr6:117923449-117923967	GM12878	blood:	n/a	chr6:117923540-117923549
47	RFX5	chr6:117923179-117924247	GM12878	blood:	n/a	n/a
48	NR2F2	chr6:117923276-117924399	K562	blood:	n/a	n/a
49	EGR1	chr6:117923508-117923872	K562	blood:	n/a	chr6:117923684-117923697 chr6:117923696-117923705
50	USF1	chr6:117923540-117924069	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:117919537..117925760-chr6:117993513..117997816,10	K562	blood:
2	chr6:117798788..117807313-chr6:117921918..117925735,11	MCF-7	breast:
3	chr6:117803575..117805462-chr6:117921337..117926516,4	K562	blood:
4	chr6:117778227..117782608-chr6:117922454..117926248,4	MCF-7	breast:
5	chr6:117803211..117805462-chr6:117921337..117926538,8	K562	blood:
6	chr6:117919854..117927630-chr6:117992313..117999313,9	K562	blood:
7	chr6:117802223..117804604-chr6:117922456..117924196,2	MCF-7	breast:
8	chr6:117921339..117924676-chr6:117954310..117957194,3	MCF-7	breast:
9	chr6:32935829..32936600-chr6:117923280..117923937,2	Hela-S3	cervix:

Variant related genes	Relation type
GOPC	TF binding region
ENSG00000204257	Chromatin interaction
ENSG00000164465	Chromatin interaction
ENSG00000207461	Chromatin interaction
ENSG00000218233	Chromatin interaction
ENSG00000153989	Chromatin interaction
ENSG00000204256	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10457315	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10457318	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10872153	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12205963	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1501474	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1532680	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1759	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1967193	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967194	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2062663	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2071825	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2088870	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs210617	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs210630	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs210633	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs210637	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs210639	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs210642	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4946265	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4946267	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4946269	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4946273	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67663020	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9285425	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9285426	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9320612	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9320614	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9320616	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9320617	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9374671	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374674	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9387491	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401014	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401019	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9401023	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9489223	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9489238	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9765895	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9767060	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117920000-117924000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:117920400-117924200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:117920400-117924200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:117920400-117924200	Active TSS	NHLF	lung
5	chr6:117920600-117924000	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr6:117920600-117924200	Active TSS	HSMMtube	muscle
7	chr6:117920600-117924200	Active TSS	NHDF-Ad	bronchial
8	chr6:117920600-117924400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:117920800-117924200	Active TSS	A549	lung
10	chr6:117920800-117924200	Active TSS	GM12878-XiMat	blood
11	chr6:117921200-117924200	Active TSS	Hela-S3	cervix
12	chr6:117921400-117924000	Active TSS	NH-A	brain
13	chr6:117921400-117924000	Active TSS	Osteobl	bone
14	chr6:117921400-117924200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:117921400-117924200	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr6:117921400-117924400	Active TSS	Ovary	ovary
17	chr6:117921400-117924400	Active TSS	Rectal Smooth Muscle	rectum
18	chr6:117921400-117924600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr6:117921400-117924600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:117921400-117924600	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:117921600-117924000	Active TSS	Muscle Satellite Cultured Cells	--
22	chr6:117921600-117924000	Active TSS	HMEC	breast
23	chr6:117921600-117924000	Active TSS	K562	blood
24	chr6:117921600-117924200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:117921600-117924600	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr6:117921600-117924600	Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr6:117921800-117924000	Active TSS	Fetal Thymus	thymus
28	chr6:117921800-117924000	Active TSS	HSMM	muscle
29	chr6:117921800-117924200	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr6:117921800-117924200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:117921800-117924200	Active TSS	Fetal Intestine Large	intestine
32	chr6:117921800-117924200	Active TSS	Fetal Intestine Small	intestine
33	chr6:117921800-117924200	Active TSS	Fetal Kidney	kidney
34	chr6:117921800-117924200	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr6:117921800-117924200	Active TSS	Thymus	Thymus
36	chr6:117921800-117924200	Active TSS	NHEK	skin
37	chr6:117921800-117924400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:117921800-117924400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:117921800-117924400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:117921800-117924400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:117921800-117924400	Active TSS	Fetal Brain Female	brain
42	chr6:117921800-117924400	Active TSS	Fetal Stomach	stomach
43	chr6:117921800-117924600	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr6:117921800-117924600	Active TSS	Right Ventricle	heart
45	chr6:117922000-117923800	Active TSS	Fetal Muscle Leg	muscle
46	chr6:117922000-117924000	Active TSS	Colon Smooth Muscle	Colon
47	chr6:117922000-117924200	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr6:117922000-117924400	Active TSS	H1 Cell Line	embryonic stem cell
49	chr6:117922200-117923800	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr6:117922200-117924000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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