Variant report

Variant	rs3799840
Chromosome Location	chr6:109702646-109702647
allele	A/T
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	chr6:109702460-109704704	GM12892	blood:	n/a	n/a
2	FOXM1	chr6:109702535-109703198	GM12878	blood:	n/a	n/a
3	RUNX3	chr6:109702179-109704771	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:109701931-109705038	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:109702612-109704685	K562	blood:	n/a	n/a
6	TAL1	chr6:109702272-109704867	K562	blood:	n/a	n/a
7	POLR2A	chr6:109702590-109704801	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr6:109702006-109705187	IMR90	lung:	n/a	n/a
9	POLR2A	chr6:109702633-109704704	PFSK-1	brain:	n/a	n/a
10	SIN3A	chr6:109702357-109704764	H1-hESC	embryonic stem cell:	n/a	chr6:109703696-109703705 chr6:109704028-109704037 chr6:109704026-109704035
11	TBP	chr6:109702428-109705046	K562	blood:	n/a	n/a
12	POLR2A	chr6:109702411-109704615	GM19193	blood:	n/a	n/a
13	POLR2A	chr6:109702616-109704609	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:109702269-109704801	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr6:109702256-109706422	HepG2	liver:	n/a	n/a
16	WRNIP1	chr6:109702639-109702970	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:109702327-109703835	GM12891	blood:	n/a	n/a
18	MAX	chr6:109702272-109705035	Hela-S3	cervix:	n/a	chr6:109704234-109704247 chr6:109704025-109704034 chr6:109704234-109704249 chr6:109704236-109704245 chr6:109703697-109703706 chr6:109704235-109704246 chr6:109704232-109704247 chr6:109704237-109704246 chr6:109704236-109704246 chr6:109704236-109704246 chr6:109704025-109704038 chr6:109704026-109704037 chr6:109704235-109704246 chr6:109704234-109704247 chr6:109704235-109704245 chr6:109704027-109704036 chr6:109704236-109704246
19	POLR2A	chr6:109702253-109704751	GM19099	blood:	n/a	n/a
20	SREBP1	chr6:109702206-109705167	GM12878	blood:	n/a	chr6:109703696-109703706 chr6:109703697-109703706 chr6:109703697-109703706
21	NFATC1	chr6:109702240-109703217	GM12878	blood:	n/a	n/a
22	POLR2A	chr6:109702615-109702985	HCT-116	colon:	n/a	n/a
23	POLR2A	chr6:109702632-109703260	GM12891	blood:	n/a	n/a
24	POLR2A	chr6:109702618-109704673	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr6:109685661-109704818	K562	blood:	n/a	n/a
26	POLR2A	chr6:109702210-109704750	PANC-1	pancreas:	n/a	n/a
27	EP300	chr6:109702381-109703146	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:109701825-109704828	GM12878	blood:	n/a	n/a
29	UBTF	chr6:109702313-109703830	K562	blood:	n/a	n/a
30	MXI1	chr6:109702311-109704968	GM12878	blood:	n/a	chr6:109704028-109704037 chr6:109704235-109704244 chr6:109704237-109704246 chr6:109703696-109703705
31	POLR2A	chr6:109701893-109704574	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:109702315-109705017	K562	blood:	n/a	n/a
33	POLR2A	chr6:109702285-109704720	GM12892	blood:	n/a	n/a
34	SIN3AK20	chr6:109702239-109704960	MCF-7	breast:	n/a	n/a
35	TBL1XR1	chr6:109700742-109703004	K562	blood:	n/a	n/a
36	POLR2A	chr6:109702388-109704682	GM18951	blood:	n/a	n/a
37	RFX5	chr6:109702409-109702727	K562	blood:	n/a	n/a
38	SIN3A	chr6:109702340-109704619	GM12878	blood:	n/a	chr6:109703696-109703705 chr6:109704028-109704037 chr6:109704026-109704035
39	CHD1	chr6:109700488-109705195	IMR90	lung:	n/a	n/a
40	PML	chr6:109702523-109704878	GM12878	blood:	n/a	n/a
41	RELA	chr6:109702405-109704748	GM12891	blood:	n/a	n/a
42	UBTF	chr6:109702281-109704781	K562	blood:	n/a	n/a
43	POLR2A	chr6:109702617-109704625	GM12891	blood:	n/a	n/a
44	MYC	chr6:109702295-109705003	K562	blood:	n/a	chr6:109704234-109704247 chr6:109704025-109704034 chr6:109704234-109704249 chr6:109704236-109704245 chr6:109703697-109703706 chr6:109704235-109704246 chr6:109704232-109704247 chr6:109704237-109704246 chr6:109704236-109704246 chr6:109704236-109704246 chr6:109704025-109704038 chr6:109704026-109704037 chr6:109704235-109704246 chr6:109704234-109704247 chr6:109704235-109704245 chr6:109704027-109704036 chr6:109704236-109704246
45	HCFC1	chr6:109702080-109705297	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr6:109701692-109705043	K562	blood:	n/a	n/a
47	POLR2A	chr6:109702586-109704681	GM12891	blood:	n/a	n/a
48	POLR2A	chr6:109702503-109704837	MCF10A-Er-Src	breast:	n/a	n/a
49	ELK1	chr6:109702557-109703111	GM12878	blood:	n/a	n/a
50	JUND	chr6:109702237-109705161	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:109662626..109665384-chr6:109701229..109703998,3	MCF-7	breast:
2	chr6:109414172..109420012-chr6:109700263..109705604,12	MCF-7	breast:
3	chr6:109613797..109616312-chr6:109702118..109704634,2	MCF-7	breast:
4	chr6:109554938..109560362-chr6:109702019..109707132,8	K562	blood:
5	chr6:109702383..109706611-chr6:109760202..109762116,4	K562	blood:
6	chr6:109414769..109417470-chr6:109702121..109705671,6	MCF-7	breast:
7	chr6:109699708..109703613-chr6:109762807..109765058,4	K562	blood:
8	chr6:109414834..109419474-chr6:109701430..109708028,12	K562	blood:
9	chr11:118134617..118135243-chr6:109702639..109703522,2	Hela-S3	cervix:
10	chr6:109556893..109560362-chr6:109702019..109704753,3	K562	blood:
11	chr6:109702597..109705942-chr6:109803330..109806291,3	K562	blood:
12	chr6:109702022..109707287-chr6:109760251..109763953,8	MCF-7	breast:
13	chr6:109702065..109705528-chr6:109760483..109765471,8	MCF-7	breast:
14	chr6:109628891..109631970-chr6:109702157..109703919,3	K562	blood:
15	chr6:109624351..109631970-chr6:109702157..109706422,11	K562	blood:
16	chr6:109610868..109612861-chr6:109702210..109704800,2	K562	blood:
17	chr6:109414590..109417855-chr6:109700035..109707147,9	K562	blood:
18	chr6:109623091..109628183-chr6:109700606..109706462,9	K562	blood:
19	chr6:109659415..109661984-chr6:109702237..109705687,4	MCF-7	breast:
20	chr6:109613644..109615634-chr6:109701677..109704002,2	K562	blood:

Variant related genes	Relation type
CD164	TF binding region
ENSG00000260273	TF binding region
ENSG00000238474	Chromatin interaction
ENSG00000183137	Chromatin interaction
ENSG00000185250	Chromatin interaction
ENSG00000201023	Chromatin interaction
ENSG00000243587	Chromatin interaction
ENSG00000112365	Chromatin interaction
ENSG00000135587	Chromatin interaction
ENSG00000219700	Chromatin interaction
ENSG00000080546	Chromatin interaction
ENSG00000149573	Chromatin interaction
ENSG00000203799	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11753645	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11757877	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12524502	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12528566	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12528712	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13192476	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13195517	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13199519	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13203252	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1322818	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2275652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34131679	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34292461	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34320275	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35452836	0.85[EUR][1000 genomes]
rs35969918	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3757238	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3799835	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4428538	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61076041	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61233650	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61318425	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67857472	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6929208	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3799840	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs3799840	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs3799840	SMPD2	cis	Whole Blood	GTEx
rs3799840	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs3799840	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109697800-109702800	Weak transcription	Spleen	Spleen
2	chr6:109700200-109705600	Active TSS	Stomach Smooth Muscle	stomach
3	chr6:109700400-109705200	Active TSS	Right Ventricle	heart
4	chr6:109700600-109703000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:109700600-109703000	Active TSS	Right Atrium	heart
6	chr6:109700600-109704800	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr6:109700600-109704800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:109700600-109704800	Active TSS	Fetal Intestine Small	intestine
9	chr6:109700600-109704800	Active TSS	Fetal Muscle Leg	muscle
10	chr6:109700600-109704800	Active TSS	GM12878-XiMat	blood
11	chr6:109700600-109705000	Active TSS	Left Ventricle	heart
12	chr6:109700600-109705800	Active TSS	Ovary	ovary
13	chr6:109700600-109706000	Active TSS	Colonic Mucosa	Colon
14	chr6:109700600-109706200	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr6:109700800-109702800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:109700800-109703000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:109700800-109704800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:109700800-109704800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:109700800-109704800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:109700800-109704800	Active TSS	Primary T cells fromperipheralblood	blood
21	chr6:109700800-109704800	Active TSS	Fetal Intestine Large	intestine
22	chr6:109700800-109704800	Active TSS	NHLF	lung
23	chr6:109700800-109705800	Active TSS	Psoas Muscle	Psoas
24	chr6:109701000-109704600	Active TSS	Fetal Thymus	thymus
25	chr6:109701000-109704600	Active TSS	Hela-S3	cervix
26	chr6:109701000-109705000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:109701200-109704600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:109701200-109704800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:109701200-109704800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:109701200-109704800	Active TSS	Stomach Mucosa	stomach
31	chr6:109701200-109705200	Active TSS	Fetal Muscle Trunk	muscle
32	chr6:109701400-109704600	Active TSS	Aorta	Aorta
33	chr6:109701400-109704600	Active TSS	Small Intestine	intestine
34	chr6:109701400-109704800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:109701400-109704800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:109701400-109704800	Active TSS	Placenta	Placenta
37	chr6:109701400-109704800	Active TSS	NHDF-Ad	bronchial
38	chr6:109701400-109705200	Active TSS	H1 Cell Line	embryonic stem cell
39	chr6:109701400-109705600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:109701600-109704600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr6:109701600-109704600	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr6:109701600-109704600	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr6:109701600-109704600	Active TSS	Muscle Satellite Cultured Cells	--
44	chr6:109701600-109704600	Active TSS	Duodenum Mucosa	Duodenum
45	chr6:109701600-109704600	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr6:109701600-109704800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:109701600-109704800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:109701600-109704800	Active TSS	Adipose Nuclei	Adipose
49	chr6:109701600-109704800	Active TSS	Brain Substantia Nigra	brain
50	chr6:109701600-109704800	Active TSS	Colon Smooth Muscle	Colon

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