Variant report

Variant	rs35902873
Chromosome Location	chr6:28058949-28058950
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:183)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28058899-28059155	MCF-7	breast:	n/a	n/a
2	CTCF	chr6:28058860-28059010	AG04449	skin:	n/a	n/a
3	GABPA	chr6:28058638-28059216	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr6:28058461-28059270	U87	brain:	n/a	n/a
5	CTCF	chr6:28058800-28058950	SK-N-SH_RA	brain:	n/a	chr6:28058843-28058856
6	MAX	chr6:28058810-28059092	SK-N-SH	brain:	n/a	n/a
7	MXI1	chr6:28058448-28059996	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr6:28057384-28059244	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:28058461-28059324	U87	brain:	n/a	n/a
10	GABPA	chr6:28058677-28059158	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr6:28058657-28059128	U87	brain:	n/a	n/a
12	POLR2A	chr6:28058753-28059044	HCT-116	colon:	n/a	n/a
13	POLR2A	chr6:28058633-28059141	SK-N-SH	brain:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28058911-28058961	K562	blood:	n/a
2	chr6:28058911-28058961	AG10803	skin:	n/a
3	chr6:28058918-28058968	Jurkat	blood:	n/a
4	chr6:28058918-28058968	AG09309	skin:	n/a
5	chr6:28058911-28058961	HRCEpiC	kidney:	n/a
6	chr6:28058911-28058961	SK-N-SH	brain:	n/a
7	chr6:28058909-28058959	A549	lung:	n/a
8	chr6:28058909-28058959	HL-60	blood:	n/a
9	chr6:28058911-28058961	HCPEpiC	choroid plexus:	n/a
10	chr6:28058918-28058968	GM12891	blood:	n/a
11	chr6:28058918-28058968	PFSK-1	brain:	n/a
12	chr6:28058918-28058968	RPTEC	kidney:	n/a
13	chr6:28058911-28058961	RPTEC	kidney:	n/a
14	chr6:28058918-28058968	Caco-2	colon:	n/a
15	chr6:28058918-28058968	NT2-D1	testis:	n/a
16	chr6:28058918-28058968	BE2_C	brain:	n/a
17	chr6:28058911-28058961	NB4	blood:	n/a
18	chr6:28058918-28058968	GM12892	blood:	n/a
19	chr6:28058909-28058959	PFSK-1	brain:	n/a
20	chr6:28058909-28058959	IMR90	lung:	fetal
21	chr6:28058918-28058968	SK-N-SH	brain:	n/a
22	chr6:28058909-28058959	NHBE	bronchial:	n/a
23	chr6:28058909-28058959	HepG2	liver:	n/a
24	chr6:28058909-28058959	RPTEC	kidney:	n/a
25	chr6:28058918-28058968	ovcar-3	ovarian:	n/a
26	chr6:28058909-28058959	AG04450	lung:	fetal
27	chr6:28058911-28058961	MCF10A-Er-Src	breast:	n/a
28	chr6:28058909-28058959	NB4	blood:	n/a
29	chr6:28058909-28058959	GM19239	blood:	n/a
30	chr6:28058911-28058961	AG04450	lung:	fetal
31	chr6:28058909-28058959	GM06990	blood:	n/a
32	chr6:28058911-28058961	CMK	blood:	n/a
33	chr6:28058918-28058968	SAEC	small airway:	n/a
34	chr6:28058918-28058968	HEK293	kidney:	embryo
35	chr6:28058918-28058968	HCF	heart:	n/a
36	chr6:28058911-28058961	A549	lung:	n/a
37	chr6:28058909-28058959	HNPCEpiC	eye:	n/a
38	chr6:28058911-28058961	H1-hESC	embryonic stem cell:	embryo
39	chr6:28058909-28058959	Caco-2	colon:	n/a
40	chr6:28058918-28058968	HNPCEpiC	eye:	n/a
41	chr6:28058911-28058961	PFSK-1	brain:	n/a
42	chr6:28058911-28058961	GM06990	blood:	n/a
43	chr6:28058909-28058959	SK-N-MC	brain:	n/a
44	chr6:28058909-28058959	SKMC	muscle:	n/a
45	chr6:28058909-28058959	SK-N-SH_RA	brain:	n/a
46	chr6:28058918-28058968	NB4	blood:	n/a
47	chr6:28058911-28058961	SK-N-MC	brain:	n/a
48	chr6:28058918-28058968	HepG2	liver:	n/a
49	chr6:28058909-28058959	ProgFib	skin:	n/a
50	chr6:28058918-28058968	HEEpiC	esophagus:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF165-1	chr6:28058585-28059262	NONHSAT108425
2	lnc-ZKSCAN4-1	chr6:28058878-28059246	NONHSAT108426

No data

Variant related genes	Relation type
ZSCAN12P1	TF binding region
ZSCAN12P1	CpG island

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs13190888	0.81[EUR][1000 genomes]
rs13191786	0.85[EUR][1000 genomes]
rs13195291	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13197176	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13197574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13197633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13200214	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13201308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13203816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13204012	0.85[EUR][1000 genomes]
rs13205211	0.85[EUR][1000 genomes]
rs13205911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13207345	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13208096	0.85[EUR][1000 genomes]
rs13211507	0.85[EUR][1000 genomes]
rs13217984	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs33932084	0.84[EUR][1000 genomes]
rs34166054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34218844	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34243448	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34371502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34396849	0.85[EUR][1000 genomes]
rs34505829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34588114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34661125	0.85[EUR][1000 genomes]
rs34662244	0.82[EUR][1000 genomes]
rs34691223	0.85[EUR][1000 genomes]
rs34765154	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34832585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34878803	0.85[EUR][1000 genomes]
rs34950484	0.85[EUR][1000 genomes]
rs35001169	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs35072899	0.85[EUR][1000 genomes]
rs35098436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35345226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35656932	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs35749575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35781323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35952432	0.90[EUR][1000 genomes]
rs56075693	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56189111	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs66886492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67297533	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67998226	0.85[EUR][1000 genomes]
rs68188794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71537572	1.00[AFR][1000 genomes]
rs71559070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71559072	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72846780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72846794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72854513	1.00[AFR][1000 genomes];0.85[EUR][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	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35902873	AL022393.7	cis	Muscle Skeletal	GTEx
rs35902873	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs35902873	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs35902873	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28049600-28059200	Weak transcription	Fetal Brain Male	brain
2	chr6:28049600-28063000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:28050800-28061200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:28053200-28059200	ZNF genes & repeats	Liver	Liver
5	chr6:28053400-28064600	Strong transcription	Placenta	Placenta
6	chr6:28055000-28059200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
7	chr6:28055200-28059600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
8	chr6:28055400-28059400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
9	chr6:28055400-28059800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:28055600-28059200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:28055600-28059200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
12	chr6:28056200-28059400	Weak transcription	HepG2	liver
13	chr6:28057200-28059000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr6:28057400-28059400	ZNF genes & repeats	Fetal Intestine Large	intestine
15	chr6:28057800-28060400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:28057800-28065800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:28058000-28060200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:28058000-28060400	Weak transcription	NHEK	skin
19	chr6:28058000-28060600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:28058000-28064800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:28058200-28062200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:28058200-28062200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr6:28058200-28072200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:28058400-28059400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:28058400-28059400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:28058400-28059400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:28058400-28059400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr6:28058400-28060800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:28058400-28061200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:28058600-28059000	Active TSS	Ovary	ovary
31	chr6:28058600-28059200	Active TSS	Muscle Satellite Cultured Cells	--
32	chr6:28058600-28059200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:28058600-28059200	Active TSS	Colon Smooth Muscle	Colon
34	chr6:28058600-28059200	Active TSS	Fetal Kidney	kidney
35	chr6:28058600-28059200	Active TSS	Fetal Stomach	stomach
36	chr6:28058600-28059200	Active TSS	Placenta Amnion	Placenta Amnion
37	chr6:28058600-28059200	Active TSS	Stomach Smooth Muscle	stomach
38	chr6:28058600-28059200	Active TSS	NHLF	lung
39	chr6:28058600-28059400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:28058600-28059400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:28058600-28059400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:28058600-28059400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:28058600-28059400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:28058600-28059400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr6:28058600-28059400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:28058600-28059400	Active TSS	Brain Angular Gyrus	brain
47	chr6:28058600-28059400	Active TSS	Brain Anterior Caudate	brain
48	chr6:28058600-28059400	Active TSS	Brain Cingulate Gyrus	brain
49	chr6:28058600-28059400	Active TSS	Brain Germinal Matrix	brain
50	chr6:28058600-28059400	Active TSS	Brain Hippocampus Middle	brain

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