Variant report

Variant	rs1890809
Chromosome Location	chr6:28110478-28110479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28103775..28113920-chr6:28177995..28190115,32	K562	blood:
2	chr6:28109464..28110985-chr6:28218502..28221254,2	MCF-7	breast:
3	chr6:28110255..28111827-chr6:28288667..28290240,2	K562	blood:
4	chr6:28109265..28112090-chr6:28302311..28305142,2	MCF-7	breast:
5	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
6	chr6:28109273..28111011-chr6:28302779..28305242,3	MCF-7	breast:
7	chr6:27791730..27793405-chr6:28109237..28111401,3	K562	blood:
8	chr6:28109577..28112061-chr6:28128257..28130394,3	MCF-7	breast:
9	chr6:28108436..28110620-chr6:28192837..28194996,3	MCF-7	breast:
10	chr6:28109524..28111212-chr6:28366058..28368601,2	K562	blood:
11	chr6:27776967..27779185-chr6:28109334..28112184,3	K562	blood:
12	chr6:28109689..28111250-chr6:28315546..28317991,2	K562	blood:
13	chr6:28091137..28098786-chr6:28103559..28111884,14	MCF-7	breast:
14	chr6:28044713..28049958-chr6:28107484..28111355,5	K562	blood:
15	chr6:28108043..28113786-chr6:28190485..28194607,10	K562	blood:
16	chr6:27791848..27794229-chr6:28109901..28113080,3	K562	blood:
17	chr6:28109506..28111867-chr6:28218476..28220389,2	K562	blood:
18	chr6:28108695..28111169-chr6:28321228..28323056,2	K562	blood:
19	chr6:28108272..28111912-chr6:28184259..28187979,3	MCF-7	breast:
20	chr6:28109157..28111504-chr6:28323298..28325916,3	K562	blood:
21	chr6:28102723..28113786-chr6:28183725..28194756,41	K562	blood:

No data

Variant related genes	Relation type
ENSG00000187626	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000197238	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000226314	Chromatin interaction
ENSG00000272009	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000197279	Chromatin interaction
ENSG00000196812	Chromatin interaction
ENSG00000158691	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10484404	1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs1150685	0.97[EUR][1000 genomes]
rs1150697	0.90[CEU][hapmap];0.89[LWK][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs1150699	0.90[CEU][hapmap]
rs1150704	0.90[CEU][hapmap]
rs1150714	0.89[CEU][hapmap]
rs11752073	1.00[CEU][hapmap];0.82[MEX][hapmap];0.82[YRI][hapmap]
rs11758148	0.88[CEU][hapmap]
rs1233664	0.90[CEU][hapmap]
rs1233665	0.90[CEU][hapmap]
rs1233666	0.90[CEU][hapmap]
rs16893552	0.89[CEU][hapmap]
rs16893817	0.90[CEU][hapmap]
rs16893937	0.89[CEU][hapmap]
rs16901846	0.89[CEU][hapmap]
rs1736890	0.90[CEU][hapmap]
rs1736894	0.81[CEU][hapmap]
rs2281043	0.89[CEU][hapmap]
rs2622315	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3800325	0.89[CEU][hapmap]
rs4141691	0.89[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap]
rs56355079	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456811	0.89[CEU][hapmap]
rs6917759	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs6923170	0.89[CEU][hapmap]
rs6929559	1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[EUR][1000 genomes]
rs73396550	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73396583	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7739332	0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7744788	0.89[CEU][hapmap]
rs7748445	0.89[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap]
rs7767176	0.89[CEU][hapmap]
rs7769054	0.90[CEU][hapmap]
rs7769416	0.89[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap]
rs993619	0.90[CEU][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1890809	AL022393.7	cis	Thyroid	GTEx
rs1890809	ZSCAN23	cis	cerebellum	SCAN
rs1890809	PARD6B	trans	cerebellum	SCAN
rs1890809	ZNF323	cis	parietal	SCAN
rs1890809	ZNF165	cis	parietal	SCAN
rs1890809	HIST1H4C	cis	parietal	SCAN
rs1890809	ZSCAN23	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28107800-28110800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:28108000-28110600	Active TSS	Brain Anterior Caudate	brain
3	chr6:28108000-28111000	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr6:28108400-28110800	Active TSS	NHDF-Ad	bronchial
5	chr6:28109000-28110600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr6:28109000-28110600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr6:28109000-28110600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr6:28109000-28110600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:28109000-28110600	Active TSS	Brain Cingulate Gyrus	brain
10	chr6:28109000-28110600	Active TSS	A549	lung
11	chr6:28109000-28110600	Active TSS	NH-A	brain
12	chr6:28109000-28110800	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr6:28109000-28110800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:28109000-28110800	Active TSS	Muscle Satellite Cultured Cells	--
15	chr6:28109000-28110800	Active TSS	Fetal Muscle Leg	muscle
16	chr6:28109000-28111000	Active TSS	H1 Cell Line	embryonic stem cell
17	chr6:28109000-28111000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:28109000-28111000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:28109000-28111000	Active TSS	Fetal Brain Female	brain
20	chr6:28109000-28111000	Active TSS	HSMMtube	muscle
21	chr6:28109000-28111000	Active TSS	NHLF	lung
22	chr6:28109000-28111400	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr6:28109200-28110600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:28109200-28110600	Active TSS	H9 Cell Line	embryonic stem cell
25	chr6:28109200-28110600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:28109200-28110600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:28109200-28110600	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr6:28109200-28110600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr6:28109200-28110600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:28109200-28110600	Active TSS	Brain Angular Gyrus	brain
31	chr6:28109200-28110600	Active TSS	Brain Hippocampus Middle	brain
32	chr6:28109200-28110600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:28109200-28110600	Active TSS	Fetal Heart	heart
34	chr6:28109200-28110600	Active TSS	Left Ventricle	heart
35	chr6:28109200-28110600	Active TSS	Ovary	ovary
36	chr6:28109200-28110600	Active TSS	Hela-S3	cervix
37	chr6:28109200-28110600	Bivalent/Poised TSS	HepG2	liver
38	chr6:28109200-28110600	Active TSS	HSMM	muscle
39	chr6:28109200-28110600	Active TSS	Osteobl	bone
40	chr6:28109200-28110800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr6:28109200-28110800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:28109200-28110800	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr6:28109200-28110800	Active TSS	Fetal Kidney	kidney
44	chr6:28109200-28111000	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr6:28109200-28111000	Active TSS	Right Ventricle	heart
46	chr6:28109200-28111200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:28109200-28111200	Active TSS	Psoas Muscle	Psoas
48	chr6:28109200-28112000	Active TSS	Aorta	Aorta
49	chr6:28109400-28110600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:28109400-28110600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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