Variant report

Variant	rs10484404
Chromosome Location	chr6:28055495-28055496
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28055389-28056472	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:28055424-28055677	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28054146..28055764-chr6:28072126..28074128,2	K562	blood:
2	chr6:28047399..28050542-chr6:28051923..28057231,4	MCF-7	breast:
3	chr6:28049008..28053394-chr6:28054919..28058473,6	MCF-7	breast:
4	chr6:28047913..28051449-chr6:28052832..28058819,8	K562	blood:
5	chr6:28053744..28056294-chr6:28058475..28060546,2	MCF-7	breast:

No data

Variant related genes	Relation type
ZSCAN12P1	TF binding region
ENSG00000272009	Chromatin interaction
ENSG00000197279	Chromatin interaction
ENSG00000219891	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1150685	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1150697	0.90[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs1150699	0.90[CEU][hapmap]
rs1150704	0.90[CEU][hapmap]
rs1150722	1.00[JPT][hapmap]
rs1150723	1.00[JPT][hapmap]
rs1150725	1.00[JPT][hapmap]
rs11752073	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap]
rs11758148	0.88[CEU][hapmap]
rs1225600	1.00[JPT][hapmap]
rs1233664	0.90[CEU][hapmap]
rs1233665	0.90[CEU][hapmap]
rs1233666	0.90[CEU][hapmap]
rs1679723	1.00[JPT][hapmap]
rs16893552	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16893817	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs16901846	0.89[CEU][hapmap]
rs1736890	0.90[CEU][hapmap]
rs1736892	1.00[JPT][hapmap]
rs1736894	0.81[CEU][hapmap]
rs1778510	1.00[JPT][hapmap]
rs1890809	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]
rs2622315	1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2799076	1.00[JPT][hapmap]
rs3757183	1.00[JPT][hapmap]
rs4141691	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs56355079	0.97[EUR][1000 genomes]
rs6910968	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs6917759	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs6918043	1.00[JPT][hapmap]
rs6929559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396550	0.83[EUR][1000 genomes]
rs73396583	0.87[EUR][1000 genomes]
rs7739332	0.87[EUR][1000 genomes]
rs7742858	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs7747772	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7748445	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs7767176	0.89[CEU][hapmap]
rs7769054	0.90[CEU][hapmap]
rs7769416	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs993619	0.90[CEU][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10484404	ZNF323	cis	parietal	SCAN
rs10484404	ZSCAN23	cis	parietal	SCAN
rs10484404	PARD6B	trans	cerebellum	SCAN
rs10484404	HIST1H4C	cis	parietal	SCAN
rs10484404	ZSCAN23	cis	cerebellum	SCAN
rs10484404	ZNF165	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28049400-28056600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:28049400-28056800	Weak transcription	Aorta	Aorta
3	chr6:28049600-28055600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:28049600-28055600	Weak transcription	Fetal Kidney	kidney
5	chr6:28049600-28056000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr6:28049600-28056000	Weak transcription	Left Ventricle	heart
7	chr6:28049600-28056400	Weak transcription	Esophagus	oesophagus
8	chr6:28049600-28056400	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:28049600-28056600	Weak transcription	Psoas Muscle	Psoas
10	chr6:28049600-28057000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr6:28049600-28058600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:28049600-28058600	Weak transcription	Brain Substantia Nigra	brain
13	chr6:28049600-28059200	Weak transcription	Fetal Brain Male	brain
14	chr6:28049600-28063000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:28049800-28055600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:28049800-28055600	Weak transcription	Stomach Mucosa	stomach
17	chr6:28049800-28056000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr6:28049800-28056200	Weak transcription	Adipose Nuclei	Adipose
19	chr6:28049800-28056800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:28049800-28056800	Weak transcription	HSMMtube	muscle
21	chr6:28049800-28057000	Weak transcription	Fetal Heart	heart
22	chr6:28049800-28057600	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:28049800-28058600	Weak transcription	Brain Germinal Matrix	brain
24	chr6:28049800-28058600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:28050000-28055800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:28050000-28056800	Weak transcription	Brain Anterior Caudate	brain
27	chr6:28050800-28061200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:28051200-28058600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:28051600-28056000	Weak transcription	K562	blood
30	chr6:28052000-28055600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:28052800-28055600	Strong transcription	Primary B cells from peripheral blood	blood
32	chr6:28053200-28055800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:28053200-28055800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr6:28053200-28059200	ZNF genes & repeats	Liver	Liver
35	chr6:28053400-28055600	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr6:28053400-28055600	Strong transcription	Fetal Intestine Large	intestine
37	chr6:28053400-28055800	Strong transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:28053400-28055800	Strong transcription	NHEK	skin
39	chr6:28053400-28056200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:28053400-28064600	Strong transcription	Placenta	Placenta
41	chr6:28053800-28056800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:28054000-28056600	Weak transcription	Hela-S3	cervix
43	chr6:28054200-28056800	Weak transcription	Gastric	stomach
44	chr6:28054200-28056800	Weak transcription	Lung	lung
45	chr6:28054200-28058600	Weak transcription	Brain Angular Gyrus	brain
46	chr6:28054200-28058600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:28054200-28058600	Weak transcription	Ovary	ovary
48	chr6:28054200-28058600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr6:28054400-28056400	Weak transcription	Fetal Stomach	stomach
50	chr6:28054600-28057200	Strong transcription	Pancreas	Pancrea

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