Variant report

Variant	rs73402526
Chromosome Location	chr6:28227400-28227401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr6:28226842-28227442	GM12878	blood:	n/a	n/a
2	ELF1	chr6:28226888-28227607	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28227392-28227442	NHBE	bronchial:	n/a
2	chr6:28227392-28227442	IMR90	lung:	fetal
3	chr6:28227392-28227442	AG04449	skin:	fetal
4	chr6:28227392-28227442	SK-N-MC	brain:	n/a
5	chr6:28227392-28227442	Hepatocyte	liver:	n/a
6	chr6:28227392-28227442	A549	lung:	n/a
7	chr6:28227392-28227442	AG09319	gingival:	n/a
8	chr6:28227392-28227442	NT2-D1	testis:	n/a
9	chr6:28227392-28227442	K562	blood:	n/a
10	chr6:28227392-28227442	H1-hESC	embryonic stem cell:	embryo
11	chr6:28227392-28227442	ProgFib	skin:	n/a
12	chr6:28227392-28227442	NH-A	brain:	n/a
13	chr6:28227392-28227442	HL-60	blood:	n/a
14	chr6:28227392-28227442	HRPEpiC	eye:	n/a
15	chr6:28227392-28227442	HCT-116	colon:	n/a
16	chr6:28227392-28227442	HIPEpiC	eye:	n/a
17	chr6:28227392-28227442	ECC-1	luminal epithelium:	n/a
18	chr6:28227392-28227442	HCM	heart:	n/a
19	chr6:28227392-28227442	AG09309	skin:	n/a
20	chr6:28227392-28227442	AoSMC	blood vessel:	n/a
21	chr6:28227392-28227442	NHDF-neo	bronchial:	n/a
22	chr6:28227392-28227442	U87	brain:	n/a
23	chr6:28227392-28227442	GM12892	blood:	n/a
24	chr6:28227392-28227442	AG04450	lung:	fetal
25	chr6:28227392-28227442	T-47D	breast:	n/a
26	chr6:28227392-28227442	PANC-1	pancreas:	n/a
27	chr6:28227392-28227442	Hela-S3	cervix:	n/a
28	chr6:28227392-28227442	HAEpiC	amniotic membrane:	n/a
29	chr6:28227392-28227442	HCF	heart:	n/a
30	chr6:28227392-28227442	NB4	blood:	n/a
31	chr6:28227392-28227442	GM06990	blood:	n/a
32	chr6:28227392-28227442	HNPCEpiC	eye:	n/a
33	chr6:28227392-28227442	GM12878	blood:	n/a
34	chr6:28227392-28227442	LNCaP	prostate:	n/a
35	chr6:28227392-28227442	HRCEpiC	kidney:	n/a
36	chr6:28227392-28227442	CMK	blood:	n/a
37	chr6:28227392-28227442	Caco-2	colon:	n/a
38	chr6:28227392-28227442	SK-N-SH_RA	brain:	n/a
39	chr6:28227392-28227442	PrEC	prostate:	n/a
40	chr6:28227392-28227442	ovcar-3	ovarian:	n/a
41	chr6:28227392-28227442	HRE	kidney:	n/a
42	chr6:28227392-28227442	SK-N-SH	brain:	n/a
43	chr6:28227392-28227442	GM12891	blood:	n/a
44	chr6:28227392-28227442	PFSK-1	brain:	n/a
45	chr6:28227392-28227442	HPAEpiC	pulmonary alveolar:	n/a
46	chr6:28227392-28227442	SAEC	small airway:	n/a
47	chr6:28227392-28227442	GM19239	blood:	n/a
48	chr6:28227392-28227442	RPTEC	kidney:	n/a
49	chr6:28227392-28227442	HCPEpiC	choroid plexus:	n/a
50	chr6:28227392-28227442	HMEC	breast:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28219997..28223882-chr6:28224379..28228192,5	K562	blood:
2	chr6:28226019..28228390-chr6:28303494..28305290,2	K562	blood:
3	chr6:28225119..28227553-chr6:28366156..28368716,2	K562	blood:
4	chr6:28218888..28222826-chr6:28224722..28227606,3	K562	blood:

No data

Variant related genes	Relation type
ZKSCAN4	TF binding region
ZKSCAN4	CpG island
ENSG00000235109	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000158691	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2223287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57229798	0.83[AFR][1000 genomes]
rs57935190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58417073	0.83[AFR][1000 genomes]
rs58703563	0.83[AFR][1000 genomes]
rs60411265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62638674	0.83[AFR][1000 genomes]
rs6917449	0.83[AFR][1000 genomes]
rs73385824	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73385839	1.00[AMR][1000 genomes]
rs73394789	1.00[AMR][1000 genomes]
rs73396511	1.00[AMR][1000 genomes]
rs73398549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73399679	0.83[AFR][1000 genomes]
rs73400304	0.83[AFR][1000 genomes]
rs73400305	0.83[AFR][1000 genomes]
rs73400511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73400554	1.00[AMR][1000 genomes]
rs73400574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73402529	1.00[AMR][1000 genomes]
rs73402530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73402536	1.00[AMR][1000 genomes]
rs7453044	0.83[AFR][1000 genomes]
rs7767244	1.00[AMR][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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28225800-28227800	Active TSS	Colon Smooth Muscle	Colon
2	chr6:28226200-28228200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
3	chr6:28226400-28227400	Active TSS	Brain Hippocampus Middle	brain
4	chr6:28226400-28227600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:28226400-28227600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr6:28226400-28227600	ZNF genes & repeats	Liver	Liver
7	chr6:28226400-28227600	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr6:28226400-28227600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr6:28226400-28227600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr6:28226400-28227800	Active TSS	Brain Anterior Caudate	brain
11	chr6:28226600-28227400	Flanking Active TSS	Primary B cells from peripheral blood	blood
12	chr6:28226600-28227400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:28226600-28227400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:28226600-28227400	Active TSS	Brain Substantia Nigra	brain
15	chr6:28226600-28227400	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr6:28226600-28227400	Bivalent/Poised TSS	Fetal Lung	lung
17	chr6:28226600-28227400	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr6:28226600-28227400	ZNF genes & repeats	HSMM	muscle
19	chr6:28226600-28227600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:28226600-28227600	ZNF genes & repeats	Primary B cells from cord blood	blood
21	chr6:28226600-28227600	Active TSS	Brain Angular Gyrus	brain
22	chr6:28226600-28227600	Active TSS	Brain Cingulate Gyrus	brain
23	chr6:28226600-28227600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:28226600-28227600	Active TSS	Duodenum Mucosa	Duodenum
25	chr6:28226600-28227600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
26	chr6:28226600-28227600	Active TSS	Left Ventricle	heart
27	chr6:28226600-28227600	ZNF genes & repeats	HMEC	breast
28	chr6:28226600-28227600	ZNF genes & repeats	NHEK	skin
29	chr6:28226600-28227800	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr6:28226600-28228400	Active TSS	Psoas Muscle	Psoas
31	chr6:28226800-28227400	Active TSS	H1 Cell Line	embryonic stem cell
32	chr6:28226800-28227400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:28226800-28227400	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr6:28226800-28227400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:28226800-28227400	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:28226800-28227400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:28226800-28227400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:28226800-28227400	ZNF genes & repeats	Esophagus	oesophagus
39	chr6:28226800-28227400	Bivalent/Poised TSS	Fetal Brain Male	brain
40	chr6:28226800-28227400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
41	chr6:28226800-28227400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
42	chr6:28226800-28227400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
43	chr6:28226800-28227400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
44	chr6:28226800-28227400	Active TSS	Thymus	Thymus
45	chr6:28226800-28227400	ZNF genes & repeats	GM12878-XiMat	blood
46	chr6:28226800-28227400	ZNF genes & repeats	NH-A	brain
47	chr6:28226800-28227600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
48	chr6:28226800-28227600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
49	chr6:28226800-28227600	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr6:28226800-28227600	Active TSS	Colonic Mucosa	Colon

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