Variant report

Variant	rs41269289
Chromosome Location	chr6:28227145-28227146
allele	C/G
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	EGR1	chr6:28226942-28227152	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
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	POLR2A	chr6:28226862-28227172	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:28226786-28227157	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr6:28227011-28227300	MCF-7	breast:	n/a	n/a
8	POLR2A	chr6:28226876-28227200	GM12878	blood:	n/a	n/a
9	HMGN3	chr6:28227039-28227156	K562	blood:	n/a	n/a
10	MYC	chr6:28226999-28227151	HUVEC	blood vessel:	n/a	n/a
11	ELF1	chr6:28226888-28227607	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28227127-28227177	HIPEpiC	eye:	n/a
2	chr6:28227127-28227177	SK-N-MC	brain:	n/a
3	chr6:28227127-28227177	T-47D	breast:	n/a
4	chr6:28227127-28227177	HNPCEpiC	eye:	n/a
5	chr6:28227127-28227177	Hela-S3	cervix:	n/a
6	chr6:28227127-28227177	HRCEpiC	kidney:	n/a
7	chr6:28227127-28227177	HEEpiC	esophagus:	n/a
8	chr6:28227127-28227177	AG09309	skin:	n/a
9	chr6:28227127-28227177	NHDF-neo	bronchial:	n/a
10	chr6:28227127-28227177	HEK293	kidney:	embryo
11	chr6:28227127-28227177	HCPEpiC	choroid plexus:	n/a
12	chr6:28227127-28227177	AG10803	skin:	n/a
13	chr6:28227127-28227177	HL-60	blood:	n/a
14	chr6:28227127-28227177	RPTEC	kidney:	n/a
15	chr6:28227127-28227177	HPAEpiC	pulmonary alveolar:	n/a
16	chr6:28227127-28227177	AoSMC	blood vessel:	n/a
17	chr6:28227127-28227177	PrEC	prostate:	n/a
18	chr6:28227127-28227177	GM06990	blood:	n/a
19	chr6:28227127-28227177	GM12892	blood:	n/a
20	chr6:28227127-28227177	A549	lung:	n/a
21	chr6:28227127-28227177	U87	brain:	n/a
22	chr6:28227127-28227177	HCT-116	colon:	n/a
23	chr6:28227127-28227177	CMK	blood:	n/a
24	chr6:28227127-28227177	SK-N-SH_RA	brain:	n/a
25	chr6:28227127-28227177	HepG2	liver:	n/a
26	chr6:28227127-28227177	ovcar-3	ovarian:	n/a
27	chr6:28227127-28227177	Jurkat	blood:	n/a
28	chr6:28227127-28227177	BE2_C	brain:	n/a
29	chr6:28227127-28227177	HUVEC	blood vessel:	n/a
30	chr6:28227127-28227177	HRPEpiC	eye:	n/a
31	chr6:28227127-28227177	GM12878	blood:	n/a
32	chr6:28227127-28227177	AG09319	gingival:	n/a
33	chr6:28227127-28227177	HCM	heart:	n/a
34	chr6:28227127-28227177	AG04450	lung:	fetal
35	chr6:28227127-28227177	GM19239	blood:	n/a
36	chr6:28227127-28227177	H1-hESC	embryonic stem cell:	embryo
37	chr6:28227127-28227177	MCF-7	breast:	n/a
38	chr6:28227127-28227177	Caco-2	colon:	n/a
39	chr6:28227127-28227177	AG04449	skin:	fetal
40	chr6:28227127-28227177	K562	blood:	n/a
41	chr6:28227127-28227177	NHBE	bronchial:	n/a
42	chr6:28227127-28227177	GM12891	blood:	n/a
43	chr6:28227127-28227177	ECC-1	luminal epithelium:	n/a
44	chr6:28227127-28227177	BJ	skin:	n/a
45	chr6:28227127-28227177	MCF10A-Er-Src	breast:	n/a
46	chr6:28227127-28227177	HCF	heart:	n/a
47	chr6:28227127-28227177	HAEpiC	amniotic membrane:	n/a
48	chr6:28227127-28227177	LNCaP	prostate:	n/a
49	chr6:28227127-28227177	HRE	kidney:	n/a
50	chr6:28227127-28227177	PANC-1	pancreas:	n/a

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:

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

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1150710	1.00[ASN][1000 genomes]
rs11546572	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2079705	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs41269285	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41269287	1.00[ASN][1000 genomes]
rs41269291	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41270579	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs41270589	1.00[AFR][1000 genomes]
rs4540253	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61744109	1.00[ASN][1000 genomes]
rs62620226	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72844204	1.00[AFR][1000 genomes]
rs72844212	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72844218	1.00[AFR][1000 genomes]
rs72844220	1.00[AFR][1000 genomes]
rs72846777	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72846788	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72846792	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72846797	1.00[ASN][1000 genomes]
rs72846802	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72848793	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849204	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849206	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849210	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849214	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849222	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72850297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72850298	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72850299	1.00[AFR][1000 genomes]
rs72850300	1.00[AFR][1000 genomes]
rs72850302	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72851105	1.00[ASN][1000 genomes]
rs72851135	1.00[ASN][1000 genomes]
rs72851138	1.00[ASN][1000 genomes]
rs72851139	1.00[ASN][1000 genomes]
rs72851156	1.00[ASN][1000 genomes]
rs72851158	1.00[ASN][1000 genomes]
rs72851160	1.00[ASN][1000 genomes]
rs72851161	1.00[ASN][1000 genomes]
rs72851168	1.00[ASN][1000 genomes]
rs72851173	1.00[AFR][1000 genomes]
rs72851179	1.00[AFR][1000 genomes]
rs72851182	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72854503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854506	1.00[ASN][1000 genomes]
rs72854515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854521	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72854522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854524	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72854525	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854527	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854531	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854533	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854535	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72854536	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72854542	0.85[AMR][1000 genomes]
rs72854546	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72854553	0.85[AMR][1000 genomes]
rs72854556	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7752415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28225800-28227800	Active TSS	Colon Smooth Muscle	Colon
2	chr6:28226200-28227200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:28226200-28228200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
4	chr6:28226400-28227200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:28226400-28227200	Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr6:28226400-28227400	Active TSS	Brain Hippocampus Middle	brain
7	chr6:28226400-28227600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:28226400-28227600	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr6:28226400-28227600	ZNF genes & repeats	Liver	Liver
10	chr6:28226400-28227600	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr6:28226400-28227600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr6:28226400-28227600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr6:28226400-28227800	Active TSS	Brain Anterior Caudate	brain
14	chr6:28226600-28227200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr6:28226600-28227200	Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr6:28226600-28227200	Bivalent/Poised TSS	Fetal Heart	heart
17	chr6:28226600-28227200	Active TSS	Rectal Smooth Muscle	rectum
18	chr6:28226600-28227200	Active TSS	Right Ventricle	heart
19	chr6:28226600-28227200	Flanking Active TSS	Osteobl	bone
20	chr6:28226600-28227400	Flanking Active TSS	Primary B cells from peripheral blood	blood
21	chr6:28226600-28227400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:28226600-28227400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:28226600-28227400	Active TSS	Brain Substantia Nigra	brain
24	chr6:28226600-28227400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr6:28226600-28227400	Bivalent/Poised TSS	Fetal Lung	lung
26	chr6:28226600-28227400	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr6:28226600-28227400	ZNF genes & repeats	HSMM	muscle
28	chr6:28226600-28227600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:28226600-28227600	ZNF genes & repeats	Primary B cells from cord blood	blood
30	chr6:28226600-28227600	Active TSS	Brain Angular Gyrus	brain
31	chr6:28226600-28227600	Active TSS	Brain Cingulate Gyrus	brain
32	chr6:28226600-28227600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:28226600-28227600	Active TSS	Duodenum Mucosa	Duodenum
34	chr6:28226600-28227600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
35	chr6:28226600-28227600	Active TSS	Left Ventricle	heart
36	chr6:28226600-28227600	ZNF genes & repeats	HMEC	breast
37	chr6:28226600-28227600	ZNF genes & repeats	NHEK	skin
38	chr6:28226600-28227800	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr6:28226600-28228400	Active TSS	Psoas Muscle	Psoas
40	chr6:28226800-28227200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:28226800-28227200	Active TSS	Primary T cells from cord blood	blood
42	chr6:28226800-28227200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
43	chr6:28226800-28227200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr6:28226800-28227200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:28226800-28227200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr6:28226800-28227200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
47	chr6:28226800-28227200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
48	chr6:28226800-28227200	Active TSS	Placenta Amnion	Placenta Amnion
49	chr6:28226800-28227400	Active TSS	H1 Cell Line	embryonic stem cell
50	chr6:28226800-28227400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung

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