Variant report

Variant	rs10456362
Chromosome Location	chr6:28221816-28221817
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POU2F2	chr6:28221787-28222285	GM12891	blood:	n/a	n/a
2	POLR2A	chr6:28221779-28222115	GM12891	blood:	n/a	n/a
3	POLR2A	chr6:28221750-28222150	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:28221771-28222174	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:28221616-28222224	K562	blood:	n/a	n/a
6	POLR2A	chr6:28221803-28222084	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:28221759-28222239	GM12891	blood:	n/a	n/a
8	POLR2A	chr6:28221774-28222173	GM12892	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28220144..28224072-chr6:28306303..28309254,3	K562	blood:
2	chr6:28219780..28221874-chr6:28323231..28325438,2	K562	blood:
3	chr6:28219546..28223731-chr6:28316147..28319107,5	K562	blood:
4	chr6:28218514..28221956-chr6:28302143..28305192,6	K562	blood:
5	chr6:28217166..28222171-chr6:28233596..28237356,7	MCF-7	breast:
6	chr6:28219997..28223882-chr6:28224379..28228192,5	K562	blood:
7	chr6:28219245..28221589-chr6:28221663..28224285,2	K562	blood:
8	chr6:28191711..28195552-chr6:28216768..28221883,5	MCF-7	breast:
9	chr6:28072503..28074418-chr6:28220133..28221944,2	K562	blood:
10	chr6:28103155..28106167-chr6:28220159..28222685,3	MCF-7	breast:
11	chr6:28220557..28222455-chr6:28320918..28322709,2	K562	blood:
12	chr6:28218888..28222826-chr6:28224722..28227606,3	K562	blood:

No data

Variant related genes	Relation type
ZKSCAN4	TF binding region
ENSG00000137185	Chromatin interaction
ENSG00000189134	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000189298	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1076639	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11755032	0.82[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11965538	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13200462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321505	0.93[CEU][hapmap]
rs1339899	0.82[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1419183	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1679709	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778507	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1778508	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1936365	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs213239	1.00[JPT][hapmap]
rs213241	0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs213243	1.00[JPT][hapmap]
rs213244	0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs2743554	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2743555	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2799077	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2799079	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757188	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs4713139	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs4713140	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs61127718	0.80[ASN][1000 genomes]
rs68141011	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901575	0.83[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs6905391	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6920512	0.82[CHB][hapmap];0.91[ASN][1000 genomes]
rs735765	1.00[CEU][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes]
rs7740487	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs853676	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853678	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853679	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853681	0.86[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853682	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs853685	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853687	0.81[ASN][1000 genomes]
rs853688	0.87[ASN][1000 genomes]
rs853694	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295765	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs9366717	0.93[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs9368561	0.80[EUR][1000 genomes]
rs9380051	0.81[GIH][hapmap]
rs9380064	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs9380069	0.93[CEU][hapmap];1.00[GIH][hapmap]
rs9393902	0.81[GIH][hapmap]
rs9393908	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs9461446	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9461448	0.82[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9461449	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9468287	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs9468318	0.80[CEU][hapmap]
rs9468321	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9468322	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9468342	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9468345	1.00[JPT][hapmap]
rs9986596	0.90[AMR][1000 genomes];0.99[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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs10456362	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs10456362	ZSCAN23	cis	cerebellum	SCAN
rs10456362	ZKSCAN3	cis	Skin Sun Exposed Lower leg	GTEx
rs10456362	ABT1	cis	parietal	SCAN
rs10456362	BTN3A2	trans	lymphoblastoid	seeQTL
rs10456362	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs10456362	RP5-874C20.3	cis	Thyroid	GTEx
rs10456362	RP5-874C20.3	cis	Esophagus Muscularis	GTEx
rs10456362	ZNF323	cis	parietal	SCAN
rs10456362	AL022393.7	cis	Muscle Skeletal	GTEx
rs10456362	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs10456362	LRRC16A	cis	parietal	SCAN
rs10456362	ZNF192	cis	cerebellum	SCAN
rs10456362	BTN2A1	cis	parietal	SCAN
rs10456362	ZSCAN23	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28220200-28222200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr6:28220600-28222400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:28220600-28226600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:28220600-28226600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:28220600-28226600	Weak transcription	HSMM	muscle
6	chr6:28220600-28226600	Weak transcription	NHEK	skin
7	chr6:28220600-28226800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:28220600-28226800	Weak transcription	HSMMtube	muscle
9	chr6:28220600-28226800	Weak transcription	NH-A	brain
10	chr6:28220800-28222000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:28220800-28222400	Enhancers	Hela-S3	cervix
12	chr6:28220800-28222400	Enhancers	K562	blood
13	chr6:28220800-28226400	Weak transcription	Pancreas	Pancrea
14	chr6:28220800-28226400	Weak transcription	Psoas Muscle	Psoas
15	chr6:28220800-28226400	Weak transcription	Right Atrium	heart
16	chr6:28220800-28226600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:28220800-28226600	Weak transcription	HMEC	breast
18	chr6:28220800-28226600	Weak transcription	HUVEC	blood vessel
19	chr6:28220800-28226600	Weak transcription	Osteobl	bone
20	chr6:28220800-28226800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:28220800-28226800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:28220800-28226800	Weak transcription	Lung	lung
23	chr6:28220800-28227000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:28220800-28227000	Weak transcription	Gastric	stomach
25	chr6:28221000-28222200	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr6:28221000-28222400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:28221200-28222000	Enhancers	HepG2	liver
28	chr6:28221200-28226400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:28221200-28226600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:28221400-28222200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr6:28221600-28226600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr6:28221800-28226600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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