Variant report

Variant	rs3799839
Chromosome Location	chr6:109702193-109702194
allele	C/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	RUNX3	chr6:109702179-109704771	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:109701931-109705038	GM12891	blood:	n/a	n/a
3	POLR2A	chr6:109702006-109705187	IMR90	lung:	n/a	n/a
4	MXI1	chr6:109701860-109702629	K562	blood:	n/a	n/a
5	POLR2A	chr6:109685661-109704818	K562	blood:	n/a	n/a
6	POLR2A	chr6:109701825-109704828	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:109701893-109704574	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr6:109700742-109703004	K562	blood:	n/a	n/a
9	CHD1	chr6:109700488-109705195	IMR90	lung:	n/a	n/a
10	HCFC1	chr6:109702080-109705297	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr6:109701692-109705043	K562	blood:	n/a	n/a
12	POLR2A	chr6:109701663-109705015	MCF10A-Er-Src	breast:	n/a	n/a
13	BRCA1	chr6:109701934-109704831	Hela-S3	cervix:	n/a	n/a
14	NFYB	chr6:109702161-109702646	GM12878	blood:	n/a	chr6:109702336-109702351 chr6:109702341-109702351
15	KAP1	chr6:109701822-109702494	K562	blood:	n/a	n/a
16	NFYB	chr6:109701797-109702646	Hela-S3	cervix:	n/a	chr6:109702336-109702351 chr6:109702341-109702351
17	POLR2A	chr6:109701941-109705074	PBDE	blood:	n/a	n/a
18	RAD21	chr6:109702174-109705154	SK-N-SH	brain:	n/a	chr6:109704590-109704609
19	POLR2A	chr6:109701915-109704834	GM18505	blood:	n/a	n/a
20	POLR2A	chr6:109701580-109704815	K562	blood:	n/a	n/a
21	CHD1	chr6:109701965-109704670	GM12878	blood:	n/a	n/a
22	MXI1	chr6:109700825-109705301	SK-N-SH	brain:	n/a	chr6:109704028-109704037 chr6:109704235-109704244 chr6:109704237-109704246 chr6:109703696-109703705
23	TBP	chr6:109702167-109703088	Hela-S3	cervix:	n/a	n/a
24	MXI1	chr6:109700978-109705291	IMR90	lung:	n/a	chr6:109704028-109704037 chr6:109704235-109704244 chr6:109704237-109704246 chr6:109703696-109703705
25	E2F4	chr6:109701991-109702877	MCF10A-Er-Src	breast:	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	chr6:109414769..109417470-chr6:109702121..109705671,6	MCF-7	breast:
6	chr6:109699708..109703613-chr6:109762807..109765058,4	K562	blood:
7	chr6:109414834..109419474-chr6:109701430..109708028,12	K562	blood:
8	chr6:109556893..109560362-chr6:109702019..109704753,3	K562	blood:
9	chr6:109702022..109707287-chr6:109760251..109763953,8	MCF-7	breast:
10	chr6:109702065..109705528-chr6:109760483..109765471,8	MCF-7	breast:
11	chr6:109628891..109631970-chr6:109702157..109703919,3	K562	blood:
12	chr6:109624351..109631970-chr6:109702157..109706422,11	K562	blood:
13	chr6:109485631..109488192-chr6:109700352..109702464,2	K562	blood:
14	chr6:109414590..109417855-chr6:109700035..109707147,9	K562	blood:
15	chr6:109623091..109628183-chr6:109700606..109706462,9	K562	blood:
16	chr6:109613644..109615634-chr6:109701677..109704002,2	K562	blood:

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

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10080429	0.92[EUR][1000 genomes]
rs1040284	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10457190	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1048203	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10782161	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10782162	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10872032	0.94[EUR][1000 genomes]
rs10872034	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11153171	0.86[EUR][1000 genomes]
rs11153174	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153175	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153176	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11153177	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153180	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153181	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11967108	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12190920	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12190996	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12192847	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12193493	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12197114	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12206928	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12209691	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12213313	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12524273	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12524639	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12528822	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13212766	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1322816	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546980	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1590306	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17070580	0.93[EUR][1000 genomes]
rs1923725	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236582	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2275650	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34202013	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35056702	0.93[EUR][1000 genomes]
rs36035949	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36099706	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3757234	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778475	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3778477	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3807005	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3818934	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59056467	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59906308	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68042406	0.84[EUR][1000 genomes]
rs6911838	0.81[EUR][1000 genomes]
rs6920962	0.85[EUR][1000 genomes]
rs6929023	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7372	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs752262	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7773095	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9320287	0.93[EUR][1000 genomes]
rs9480933	0.94[EUR][1000 genomes]
rs9480948	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9480951	0.93[EUR][1000 genomes]
rs9480953	0.93[EUR][1000 genomes]
rs9480955	0.93[EUR][1000 genomes]
rs9480957	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9487068	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9487094	0.93[EUR][1000 genomes]
rs9487095	0.93[EUR][1000 genomes]
rs9487097	0.88[EUR][1000 genomes]
rs9487098	0.89[EUR][1000 genomes]
rs9487100	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9885646	0.93[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3799839	SMPD2	cis	Whole Blood	GTEx
rs3799839	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs3799839	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs3799839	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs3799839	MICAL1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109684000-109702400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:109684400-109702400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:109693400-109702600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:109696800-109702400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:109697800-109702400	Weak transcription	Esophagus	oesophagus
6	chr6:109697800-109702800	Weak transcription	Spleen	Spleen
7	chr6:109698400-109702400	Weak transcription	Lung	lung
8	chr6:109699400-109702400	Weak transcription	Gastric	stomach
9	chr6:109699400-109702600	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr6:109699600-109702400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:109699600-109702400	Weak transcription	Pancreas	Pancrea
12	chr6:109699800-109702400	Transcr. at gene 5' and 3'	K562	blood
13	chr6:109700200-109702400	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr6:109700200-109705600	Active TSS	Stomach Smooth Muscle	stomach
15	chr6:109700400-109702200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr6:109700400-109702200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:109700400-109705200	Active TSS	Right Ventricle	heart
18	chr6:109700600-109702200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:109700600-109702200	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr6:109700600-109703000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:109700600-109703000	Active TSS	Right Atrium	heart
22	chr6:109700600-109704800	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr6:109700600-109704800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:109700600-109704800	Active TSS	Fetal Intestine Small	intestine
25	chr6:109700600-109704800	Active TSS	Fetal Muscle Leg	muscle
26	chr6:109700600-109704800	Active TSS	GM12878-XiMat	blood
27	chr6:109700600-109705000	Active TSS	Left Ventricle	heart
28	chr6:109700600-109705800	Active TSS	Ovary	ovary
29	chr6:109700600-109706000	Active TSS	Colonic Mucosa	Colon
30	chr6:109700600-109706200	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr6:109700800-109702600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr6:109700800-109702800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:109700800-109703000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:109700800-109704800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:109700800-109704800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:109700800-109704800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:109700800-109704800	Active TSS	Primary T cells fromperipheralblood	blood
38	chr6:109700800-109704800	Active TSS	Fetal Intestine Large	intestine
39	chr6:109700800-109704800	Active TSS	NHLF	lung
40	chr6:109700800-109705800	Active TSS	Psoas Muscle	Psoas
41	chr6:109701000-109702400	Active TSS	HepG2	liver
42	chr6:109701000-109704600	Active TSS	Fetal Thymus	thymus
43	chr6:109701000-109704600	Active TSS	Hela-S3	cervix
44	chr6:109701000-109705000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:109701200-109702600	Flanking Active TSS	Fetal Brain Female	brain
46	chr6:109701200-109704600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:109701200-109704800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:109701200-109704800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:109701200-109704800	Active TSS	Stomach Mucosa	stomach
50	chr6:109701200-109705200	Active TSS	Fetal Muscle Trunk	muscle

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