Variant report

Variant	rs12374649
Chromosome Location	chr6:27343726-27343727
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr6:27343621-27343821	K562	blood:	n/a	n/a
2	CTCF	chr6:27343600-27343750	HMEC	breast:	n/a	n/a
3	CTCF	chr6:27343580-27343730	GM12864	blood:	n/a	n/a
4	CTCF	chr6:27343580-27343730	HAc	cerebellar:	n/a	n/a
5	CTCF	chr6:27343580-27343730	HCPEpiC	choroid plexus:	n/a	n/a
6	IRF1	chr6:27342916-27343909	K562	blood:	n/a	chr6:27343629-27343650
7	CTCF	chr6:27343680-27343830	AG09319	gingival:	n/a	n/a
8	CTCF	chr6:27343600-27343750	HEK293	kidney:	n/a	n/a
9	ARID3A	chr6:27343081-27343860	K562	blood:	n/a	n/a
10	CTCF	chr6:27343600-27343750	HCPEpiC	choroid plexus:	n/a	n/a
11	RCOR1	chr6:27343565-27343839	K562	blood:	n/a	n/a
12	CTCF	chr6:27343600-27343750	HMF	breast:	n/a	n/a
13	HCFC1	chr6:27342739-27343965	Hela-S3	cervix:	n/a	n/a
14	JUND	chr6:27342802-27343844	K562	blood:	n/a	n/a
15	CTCF	chr6:27343720-27343870	HCT-116	colon:	n/a	n/a
16	CTCF	chr6:27343620-27343770	HCM	heart:	n/a	n/a
17	CTCF	chr6:27343546-27343906	K562	blood:	n/a	n/a
18	CTCF	chr6:27343580-27343730	HBMEC	blood vessel:	n/a	n/a
19	CTCF	chr6:27343700-27343850	K562	blood:	n/a	n/a
20	CTCF	chr6:27343503-27343918	K562	blood:	n/a	n/a
21	IRF1	chr6:27342902-27343906	K562	blood:	n/a	chr6:27343629-27343650
22	CTCF	chr6:27343600-27343750	AG10803	skin:	n/a	n/a
23	PRDM1	chr6:27343567-27343784	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr6:27343680-27343830	BJ	skin:	n/a	n/a
25	CTCF	chr6:27343639-27343835	K562	blood:	n/a	n/a
26	CTCF	chr6:27343660-27343810	HBMEC	blood vessel:	n/a	n/a
27	CTCF	chr6:27343620-27343770	GM12873	blood:	n/a	n/a
28	CTCF	chr6:27343708-27343809	Hela-S3	cervix:	n/a	n/a
29	IRF1	chr6:27343470-27343826	K562	blood:	n/a	chr6:27343629-27343650
30	CUX1	chr6:27343089-27343813	K562	blood:	n/a	n/a
31	CTCF	chr6:27343640-27343790	AoAF	blood vessel:	n/a	n/a
32	CTCF	chr6:27343580-27343730	HPAF	blood vessel:	n/a	n/a
33	EP300	chr6:27343073-27343820	K562	blood:	n/a	chr6:27343215-27343223
34	MAZ	chr6:27342247-27343878	K562	blood:	n/a	n/a
35	NR2F2	chr6:27342419-27343946	K562	blood:	n/a	n/a
36	MYC	chr6:27343502-27343858	K562	blood:	n/a	n/a
37	MAFK	chr6:27343009-27343866	K562	blood:	n/a	n/a
38	CTCF	chr6:27343580-27343730	HMF	breast:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27337172..27339325-chr6:27341568..27344928,3	K562	blood:
2	chr6:27342508..27344098-chr6:27729808..27732720,2	K562	blood:
3	chr6:27114024..27116946-chr6:27342885..27344567,2	K562	blood:
4	chr6:27200503..27203142-chr6:27342882..27344884,2	K562	blood:
5	chr6:27342727..27344424-chr6:27438999..27440898,2	MCF-7	breast:
6	chr6:27115446..27117075-chr6:27342528..27344567,2	K562	blood:
7	chr6:27326798..27329465-chr6:27342926..27345023,2	K562	blood:
8	chr6:27342371..27343890-chr6:27355850..27358027,2	K562	blood:
9	chr6:27342399..27344013-chr6:27374459..27376569,2	K562	blood:
10	chr6:27343258..27344900-chr6:27355145..27357535,2	MCF-7	breast:
11	chr6:27343208..27345684-chr6:27358840..27361489,2	K562	blood:

No data

Variant related genes	Relation type
ZNF204P	TF binding region
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000124613	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000204789	Chromatin interaction
ENSG00000271755	Chromatin interaction
ENSG00000237154	Chromatin interaction
ENSG00000096654	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10456051	1.00[AMR][1000 genomes]
rs10456355	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12189640	1.00[AMR][1000 genomes]
rs12191414	0.81[EUR][1000 genomes]
rs12191649	1.00[AMR][1000 genomes]
rs12192560	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12193557	1.00[AMR][1000 genomes]
rs12194341	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12194842	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12195783	1.00[AMR][1000 genomes]
rs12196452	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12196970	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12199685	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12199806	1.00[AMR][1000 genomes]
rs12202956	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12204953	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12205044	1.00[AMR][1000 genomes]
rs12209174	1.00[AMR][1000 genomes]
rs12209905	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12211931	1.00[AMR][1000 genomes]
rs12212348	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12212389	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12212632	1.00[AMR][1000 genomes]
rs12213471	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12213533	0.87[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12215289	1.00[AMR][1000 genomes]
rs12215353	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12215386	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12215878	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12374607	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16898089	0.80[AFR][1000 genomes]
rs16898738	0.80[AFR][1000 genomes]
rs28410967	0.85[EUR][1000 genomes]
rs56099947	0.84[AMR][1000 genomes]
rs60888769	0.84[AMR][1000 genomes]
rs62617138	1.00[AMR][1000 genomes]
rs71546544	0.84[AMR][1000 genomes]
rs726831	1.00[YRI][hapmap]
rs72839451	0.85[EUR][1000 genomes]
rs72839468	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72839469	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72839470	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72839471	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72839474	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72839479	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72841397	0.84[AMR][1000 genomes]
rs72841398	0.84[AMR][1000 genomes]
rs72841399	0.84[AMR][1000 genomes]
rs72841400	0.84[AMR][1000 genomes]
rs72843151	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72843177	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72843191	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72845006	0.84[AMR][1000 genomes]
rs72845008	0.84[AMR][1000 genomes]
rs72845011	0.84[AMR][1000 genomes]
rs72845012	0.84[AMR][1000 genomes]
rs72845025	0.84[AMR][1000 genomes]
rs72845027	0.84[AMR][1000 genomes]
rs72845028	0.84[AMR][1000 genomes]
rs72845030	0.84[AMR][1000 genomes]
rs72845031	0.84[AMR][1000 genomes]
rs72845208	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72845232	1.00[AMR][1000 genomes]
rs9348763	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9368509	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9379975	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9393814	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27341800-27343800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:27341800-27343800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr6:27342000-27343800	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr6:27342000-27343800	Active TSS	Aorta	Aorta
5	chr6:27342000-27343800	Active TSS	Colonic Mucosa	Colon
6	chr6:27342000-27343800	Active TSS	Ovary	ovary
7	chr6:27342000-27344000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr6:27342200-27343800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:27342200-27343800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:27342200-27343800	Active TSS	Colon Smooth Muscle	Colon
11	chr6:27342200-27343800	ZNF genes & repeats	GM12878-XiMat	blood
12	chr6:27342200-27344000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:27342200-27344000	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr6:27342200-27344000	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr6:27342400-27343800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:27342400-27343800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:27342400-27343800	Active TSS	Brain Substantia Nigra	brain
18	chr6:27342400-27343800	Active TSS	Right Atrium	heart
19	chr6:27342400-27343800	Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr6:27342400-27343800	Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr6:27342400-27344000	Active TSS	Brain Angular Gyrus	brain
22	chr6:27342400-27344000	Active TSS	Brain Hippocampus Middle	brain
23	chr6:27342400-27344000	Active TSS	Fetal Lung	lung
24	chr6:27342600-27343800	Active TSS	Stomach Smooth Muscle	stomach
25	chr6:27342800-27343800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:27343000-27343800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr6:27343000-27343800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr6:27343000-27343800	Active TSS	Thymus	Thymus
29	chr6:27343000-27343800	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
30	chr6:27343000-27345400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:27343000-27346400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr6:27343200-27343800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr6:27343200-27343800	Bivalent Enhancer	Primary B cells from cord blood	blood
34	chr6:27343200-27343800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr6:27343200-27343800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr6:27343200-27343800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:27343200-27343800	Active TSS	Fetal Stomach	stomach
38	chr6:27343200-27343800	Active TSS	HepG2	liver
39	chr6:27343200-27344000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr6:27343200-27347800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:27343200-27356200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:27343400-27343800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr6:27343400-27343800	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:27343400-27343800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:27343400-27343800	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr6:27343400-27343800	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr6:27343400-27343800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr6:27343400-27343800	Flanking Active TSS	Fetal Muscle Leg	muscle
49	chr6:27343400-27343800	Flanking Active TSS	Osteobl	bone
50	chr6:27343400-27344200	Enhancers	Dnd41	blood

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