Variant report

Variant	rs41270599
Chromosome Location	chr6:28554543-28554544
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:28554540-28554690	SK-N-SH_RA	brain:	n/a	n/a
2	GABPA	chr6:28554504-28555595	A549	lung:	n/a	n/a
3	MXI1	chr6:28554510-28555533	HepG2	liver:	n/a	n/a
4	SIN3AK20	chr6:28554535-28555724	MCF-7	breast:	n/a	n/a
5	RELA	chr6:28554500-28555495	GM19099	blood:	n/a	n/a
6	SMARCC1	chr6:28554361-28555834	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:28554261-28555399	MCF10A-Er-Src	breast:	n/a	n/a
8	SIN3A	chr6:28554102-28555617	H1-hESC	embryonic stem cell:	n/a	n/a
9	CUX1	chr6:28554538-28554709	GM12878	blood:	n/a	n/a
10	GABPA	chr6:28554233-28555766	MCF-7	breast:	n/a	n/a
11	HCFC1	chr6:28554543-28555709	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr6:28554479-28555969	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:28554052-28555628	SK-N-MC	brain:	n/a	n/a
14	REST	chr6:28554074-28555925	H1-neurons	neurons:	n/a	n/a
15	MYBL2	chr6:28554384-28555508	HepG2	liver:	n/a	n/a
16	POLR2A	chr6:28554469-28555742	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28554497-28554547	AG04450	lung:	fetal
2	chr6:28554497-28554547	HAEpiC	amniotic membrane:	n/a
3	chr6:28554497-28554547	Caco-2	colon:	n/a
4	chr6:28554497-28554547	GM12878	blood:	n/a
5	chr6:28554497-28554547	BE2_C	brain:	n/a
6	chr6:28554497-28554547	NH-A	brain:	n/a
7	chr6:28554497-28554547	RPTEC	kidney:	n/a
8	chr6:28554497-28554547	Hela-S3	cervix:	n/a
9	chr6:28554497-28554547	NT2-D1	testis:	n/a
10	chr6:28554497-28554547	GM12892	blood:	n/a
11	chr6:28554497-28554547	HRE	kidney:	n/a
12	chr6:28554497-28554547	MCF10A-Er-Src	breast:	n/a
13	chr6:28554497-28554547	HRPEpiC	eye:	n/a
14	chr6:28554497-28554547	HUVEC	blood vessel:	n/a
15	chr6:28554497-28554547	AG04449	skin:	fetal
16	chr6:28554497-28554547	HEEpiC	esophagus:	n/a
17	chr6:28554497-28554547	HL-60	blood:	n/a
18	chr6:28554497-28554547	LNCaP	prostate:	n/a
19	chr6:28554497-28554547	NHBE	bronchial:	n/a
20	chr6:28554497-28554547	ECC-1	luminal epithelium:	n/a
21	chr6:28554497-28554547	HNPCEpiC	eye:	n/a
22	chr6:28554497-28554547	BJ	skin:	n/a
23	chr6:28554497-28554547	HCPEpiC	choroid plexus:	n/a
24	chr6:28554497-28554547	HEK293	kidney:	embryo
25	chr6:28554497-28554547	AG10803	skin:	n/a
26	chr6:28554497-28554547	SKMC	muscle:	n/a
27	chr6:28554497-28554547	H1-hESC	embryonic stem cell:	embryo
28	chr6:28554497-28554547	Jurkat	blood:	n/a
29	chr6:28554497-28554547	ovcar-3	ovarian:	n/a
30	chr6:28554497-28554547	SK-N-SH_RA	brain:	n/a
31	chr6:28554497-28554547	T-47D	breast:	n/a
32	chr6:28554497-28554547	NHDF-neo	bronchial:	n/a
33	chr6:28554497-28554547	NB4	blood:	n/a
34	chr6:28554497-28554547	A549	lung:	n/a
35	chr6:28554497-28554547	GM06990	blood:	n/a
36	chr6:28554497-28554547	SAEC	small airway:	n/a
37	chr6:28554497-28554547	HMEC	breast:	n/a
38	chr6:28554497-28554547	HepG2	liver:	n/a
39	chr6:28554497-28554547	SK-N-SH	brain:	n/a
40	chr6:28554497-28554547	MCF-7	breast:	n/a
41	chr6:28554497-28554547	HCT-116	colon:	n/a
42	chr6:28554497-28554547	HCM	heart:	n/a
43	chr6:28554497-28554547	PrEC	prostate:	n/a
44	chr6:28554497-28554547	GM12891	blood:	n/a
45	chr6:28554497-28554547	Hepatocyte	liver:	n/a
46	chr6:28554497-28554547	K562	blood:	n/a
47	chr6:28554497-28554547	IMR90	lung:	fetal
48	chr6:28554497-28554547	HIPEpiC	eye:	n/a
49	chr6:28554497-28554547	PANC-1	pancreas:	n/a
50	chr6:28554497-28554547	GM19239	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:26055781..26056716-chr6:28554148..28555077,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000246350	TF binding region
SCAND3	TF binding region
SCAND3	CpG island
ENSG00000246350	CpG island
ENSG00000187837	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11963067	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13215054	0.83[AFR][1000 genomes]
rs13217047	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16901848	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17336532	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2394102	0.83[ASN][1000 genomes]
rs35051649	0.82[ASN][1000 genomes]
rs35257859	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35546888	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35778344	0.87[ASN][1000 genomes]
rs6923110	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6941188	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7742957	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7766356	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs41270599	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs41270599	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs41270599	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28552200-28554600	Flanking Active TSS	Fetal Brain Female	brain
2	chr6:28552400-28559600	Strong transcription	K562	blood
3	chr6:28553000-28558200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr6:28553200-28558200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:28553200-28558600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr6:28553600-28554600	Flanking Active TSS	HMEC	breast
7	chr6:28553800-28554600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:28553800-28556400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:28553800-28557600	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:28553800-28558200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr6:28553800-28558400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:28553800-28558400	Active TSS	H1 Cell Line	embryonic stem cell
13	chr6:28554000-28554600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:28554000-28554600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:28554000-28554600	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr6:28554000-28554600	Flanking Active TSS	Fetal Brain Male	brain
17	chr6:28554000-28554600	Enhancers	Gastric	stomach
18	chr6:28554000-28554800	Flanking Active TSS	Liver	Liver
19	chr6:28554000-28554800	Flanking Active TSS	Hela-S3	cervix
20	chr6:28554000-28554800	Flanking Active TSS	NHEK	skin
21	chr6:28554000-28555600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
22	chr6:28554000-28555600	Active TSS	Fetal Kidney	kidney
23	chr6:28554000-28555600	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr6:28554000-28555600	Active TSS	Lung	lung
25	chr6:28554000-28555600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
26	chr6:28554000-28555800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:28554000-28555800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:28554000-28555800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
29	chr6:28554000-28556000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:28554000-28556000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr6:28554000-28556200	Bivalent/Poised TSS	Brain Anterior Caudate	brain
32	chr6:28554000-28556200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:28554000-28558000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
34	chr6:28554200-28554600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:28554200-28554600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
36	chr6:28554200-28554600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
37	chr6:28554200-28554600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
38	chr6:28554200-28554600	Flanking Active TSS	Fetal Heart	heart
39	chr6:28554200-28554600	Active TSS	Fetal Lung	lung
40	chr6:28554200-28554600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
41	chr6:28554200-28554800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
42	chr6:28554200-28554800	Active TSS	Right Atrium	heart
43	chr6:28554200-28554800	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
44	chr6:28554200-28555000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr6:28554200-28555400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:28554200-28555600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
47	chr6:28554200-28555600	Active TSS	Rectal Smooth Muscle	rectum
48	chr6:28554200-28555800	Active TSS	Colonic Mucosa	Colon
49	chr6:28554200-28555800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
50	chr6:28554200-28555800	Bivalent/Poised TSS	Fetal Stomach	stomach

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