Variant report

Variant	rs72850300
Chromosome Location	chr6:28226903-28226904
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr6:28226667-28226997	GM12891	blood:	n/a	chr6:28226781-28226790 chr6:28226703-28226716
2	EGR1	chr6:28226896-28227187	GM12878	blood:	n/a	chr6:28227055-28227066 chr6:28227078-28227087 chr6:28227054-28227068 chr6:28227055-28227066 chr6:28227055-28227069 chr6:28227054-28227067 chr6:28227050-28227072 chr6:28227056-28227066 chr6:28227125-28227132 chr6:28227056-28227066
3	MTA3	chr6:28226451-28227231	GM12878	blood:	n/a	n/a
4	PML	chr6:28226842-28227442	GM12878	blood:	n/a	n/a
5	RUNX3	chr6:28226797-28227131	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:28226862-28227172	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:28226786-28227157	HUVEC	blood vessel:	n/a	n/a
8	SPI1	chr6:28226727-28226945	GM12878	blood:	n/a	chr6:28226781-28226790
9	POLR2A	chr6:28226876-28227200	GM12878	blood:	n/a	n/a
10	SPI1	chr6:28226734-28226950	GM12878	blood:	n/a	chr6:28226781-28226790
11	SPI1	chr6:28226421-28227104	GM12878	blood:	n/a	chr6:28226781-28226790 chr6:28226703-28226716
12	ELF1	chr6:28226888-28227607	GM12878	blood:	n/a	n/a
13	RUNX3	chr6:28226647-28227135	GM12878	blood:	n/a	n/a
14	SPI1	chr6:28226636-28227071	GM12891	blood:	n/a	chr6:28226781-28226790 chr6:28226703-28226716

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28226885-28226935	HCM	heart:	n/a
2	chr6:28226885-28226935	AoSMC	blood vessel:	n/a
3	chr6:28226885-28226935	AG09319	gingival:	n/a
4	chr6:28226885-28226935	HCT-116	colon:	n/a
5	chr6:28226885-28226935	RPTEC	kidney:	n/a
6	chr6:28226885-28226935	BJ	skin:	n/a
7	chr6:28226885-28226935	GM12891	blood:	n/a
8	chr6:28226885-28226935	SK-N-SH_RA	brain:	n/a
9	chr6:28226885-28226935	Hela-S3	cervix:	n/a
10	chr6:28226885-28226935	NB4	blood:	n/a
11	chr6:28226885-28226935	ProgFib	skin:	n/a
12	chr6:28226885-28226935	NH-A	brain:	n/a
13	chr6:28226885-28226935	HRCEpiC	kidney:	n/a
14	chr6:28226885-28226935	HEK293	kidney:	embryo
15	chr6:28226885-28226935	CMK	blood:	n/a
16	chr6:28226885-28226935	NHBE	bronchial:	n/a
17	chr6:28226885-28226935	SK-N-SH	brain:	n/a
18	chr6:28226885-28226935	HL-60	blood:	n/a
19	chr6:28226885-28226935	HCPEpiC	choroid plexus:	n/a
20	chr6:28226885-28226935	H1-hESC	embryonic stem cell:	embryo
21	chr6:28226885-28226935	PrEC	prostate:	n/a
22	chr6:28226885-28226935	Caco-2	colon:	n/a
23	chr6:28226885-28226935	HEEpiC	esophagus:	n/a
24	chr6:28226885-28226935	IMR90	lung:	fetal
25	chr6:28226885-28226935	ovcar-3	ovarian:	n/a
26	chr6:28226885-28226935	HepG2	liver:	n/a
27	chr6:28226885-28226935	MCF10A-Er-Src	breast:	n/a
28	chr6:28226885-28226935	BE2_C	brain:	n/a
29	chr6:28226885-28226935	GM12892	blood:	n/a
30	chr6:28226885-28226935	AG04449	skin:	fetal
31	chr6:28226885-28226935	HMEC	breast:	n/a
32	chr6:28226885-28226935	NT2-D1	testis:	n/a
33	chr6:28226885-28226935	SK-N-MC	brain:	n/a
34	chr6:28226885-28226935	PFSK-1	brain:	n/a
35	chr6:28226885-28226935	Hepatocyte	liver:	n/a
36	chr6:28226885-28226935	SAEC	small airway:	n/a
37	chr6:28226885-28226935	AG10803	skin:	n/a
38	chr6:28226885-28226935	HUVEC	blood vessel:	n/a
39	chr6:28226885-28226935	MCF-7	breast:	n/a
40	chr6:28226885-28226935	SKMC	muscle:	n/a
41	chr6:28226885-28226935	HRE	kidney:	n/a
42	chr6:28226885-28226935	HRPEpiC	eye:	n/a
43	chr6:28226885-28226935	HPAEpiC	pulmonary alveolar:	n/a
44	chr6:28226885-28226935	PANC-1	pancreas:	n/a
45	chr6:28226885-28226935	HIPEpiC	eye:	n/a
46	chr6:28226885-28226935	HAEpiC	amniotic membrane:	n/a
47	chr6:28226885-28226935	K562	blood:	n/a
48	chr6:28226885-28226935	GM06990	blood:	n/a
49	chr6:28226885-28226935	GM12878	blood:	n/a
50	chr6:28226885-28226935	Jurkat	blood:	n/a

(count:5 , 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:
5	chr6:28224904..28226983-chr6:28276563..28279040,2	K562	blood:

No data

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

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11546572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2079705	1.00[AFR][1000 genomes]
rs41269285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41269289	1.00[AFR][1000 genomes]
rs41269291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41270579	1.00[AFR][1000 genomes]
rs41270589	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4540253	1.00[AFR][1000 genomes]
rs61744109	0.83[EUR][1000 genomes]
rs62620226	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72844204	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72844212	1.00[AFR][1000 genomes]
rs72844218	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72844220	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72846777	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72846788	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72846792	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72846797	0.83[EUR][1000 genomes]
rs72846802	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72848793	1.00[AFR][1000 genomes]
rs72849204	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72849206	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72849210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72849214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72849222	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs72850297	1.00[AFR][1000 genomes]
rs72850298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72850299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72850302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72851105	0.81[EUR][1000 genomes]
rs72851135	0.84[EUR][1000 genomes]
rs72851138	0.83[EUR][1000 genomes]
rs72851139	0.83[EUR][1000 genomes]
rs72851156	0.83[EUR][1000 genomes]
rs72851158	0.83[EUR][1000 genomes]
rs72851160	0.83[EUR][1000 genomes]
rs72851161	0.83[EUR][1000 genomes]
rs72851168	0.83[EUR][1000 genomes]
rs72851173	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72851179	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72851182	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72854503	1.00[AFR][1000 genomes]
rs72854506	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72854515	1.00[AFR][1000 genomes]
rs72854521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72854522	1.00[AFR][1000 genomes]
rs72854525	1.00[AFR][1000 genomes]
rs72854527	1.00[AFR][1000 genomes]
rs72854531	1.00[AFR][1000 genomes]
rs72854533	1.00[AFR][1000 genomes]
rs72854535	1.00[AFR][1000 genomes]
rs72854536	1.00[AFR][1000 genomes]
rs72854546	1.00[AFR][1000 genomes]
rs72854556	1.00[AFR][1000 genomes]
rs7752415	1.00[AFR][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:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28220800-28227000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:28220800-28227000	Weak transcription	Gastric	stomach
3	chr6:28225800-28227800	Active TSS	Colon Smooth Muscle	Colon
4	chr6:28226200-28227200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:28226200-28228200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
6	chr6:28226400-28227200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:28226400-28227200	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr6:28226400-28227400	Active TSS	Brain Hippocampus Middle	brain
9	chr6:28226400-28227600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:28226400-28227600	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr6:28226400-28227600	ZNF genes & repeats	Liver	Liver
12	chr6:28226400-28227600	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr6:28226400-28227600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr6:28226400-28227600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr6:28226400-28227800	Active TSS	Brain Anterior Caudate	brain
16	chr6:28226600-28227000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:28226600-28227000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:28226600-28227000	Active TSS	Aorta	Aorta
19	chr6:28226600-28227000	Active TSS	Ovary	ovary
20	chr6:28226600-28227000	Active TSS	Right Atrium	heart
21	chr6:28226600-28227000	Bivalent/Poised TSS	Stomach Mucosa	stomach
22	chr6:28226600-28227000	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr6:28226600-28227000	Flanking Active TSS	NHDF-Ad	bronchial
24	chr6:28226600-28227200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr6:28226600-28227200	Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr6:28226600-28227200	Bivalent/Poised TSS	Fetal Heart	heart
27	chr6:28226600-28227200	Active TSS	Rectal Smooth Muscle	rectum
28	chr6:28226600-28227200	Active TSS	Right Ventricle	heart
29	chr6:28226600-28227200	Flanking Active TSS	Osteobl	bone
30	chr6:28226600-28227400	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr6:28226600-28227400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:28226600-28227400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:28226600-28227400	Active TSS	Brain Substantia Nigra	brain
34	chr6:28226600-28227400	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr6:28226600-28227400	Bivalent/Poised TSS	Fetal Lung	lung
36	chr6:28226600-28227400	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr6:28226600-28227400	ZNF genes & repeats	HSMM	muscle
38	chr6:28226600-28227600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:28226600-28227600	ZNF genes & repeats	Primary B cells from cord blood	blood
40	chr6:28226600-28227600	Active TSS	Brain Angular Gyrus	brain
41	chr6:28226600-28227600	Active TSS	Brain Cingulate Gyrus	brain
42	chr6:28226600-28227600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:28226600-28227600	Active TSS	Duodenum Mucosa	Duodenum
44	chr6:28226600-28227600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
45	chr6:28226600-28227600	Active TSS	Left Ventricle	heart
46	chr6:28226600-28227600	ZNF genes & repeats	HMEC	breast
47	chr6:28226600-28227600	ZNF genes & repeats	NHEK	skin
48	chr6:28226600-28227800	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr6:28226600-28228400	Active TSS	Psoas Muscle	Psoas
50	chr6:28226800-28227000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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