Variant report

Variant	rs1778477
Chromosome Location	chr6:28248594-28248595
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr6:28248547-28248627	K562	blood:	n/a	n/a
2	MAX	chr6:28248505-28248680	NB4	blood:	n/a	n/a
3	POLR2A	chr6:28248575-28248775	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr6:28248496-28250642	SK-N-SH	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27859121..27861068-chr6:28247840..28249566,2	K562	blood:
2	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
3	chr6:28193103..28195771-chr6:28247213..28248961,2	K562	blood:
4	chr6:28246460..28249146-chr6:28271252..28274232,2	K562	blood:
5	chr6:28247415..28251168-chr6:28301808..28306623,8	K562	blood:
6	chr6:28186460..28191177-chr6:28246836..28252039,7	K562	blood:
7	chr6:28248171..28250694-chr6:28301952..28304469,4	MCF-7	breast:
8	chr6:28191774..28193950-chr6:28248058..28250874,2	K562	blood:
9	chr6:28232995..28235984-chr6:28248211..28251032,3	MCF-7	breast:
10	chr6:28247781..28251138-chr6:28322226..28325499,4	K562	blood:

No data

Variant related genes	Relation type
PGBD1	TF binding region
ENSG00000233224	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000197153	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1062169	0.83[ASW][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1119211	0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1150699	0.91[GIH][hapmap]
rs1150704	0.91[GIH][hapmap]
rs1150713	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150717	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150719	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150720	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11751702	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11756111	1.00[CEU][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11757730	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11758337	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1233664	0.94[GIH][hapmap]
rs1233665	0.91[GIH][hapmap]
rs1233666	0.91[GIH][hapmap]
rs13210258	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs16893817	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16893937	0.83[GIH][hapmap]
rs1736890	0.91[GIH][hapmap]
rs1736894	0.91[GIH][hapmap]
rs1778478	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185955	1.00[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2235359	1.00[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2281043	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56053755	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456811	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456814	0.80[ASN][1000 genomes]
rs6923170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73740584	0.83[ASN][1000 genomes]
rs7741443	0.90[AMR][1000 genomes];0.93[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1778477	HIST1H4C	cis	parietal	SCAN
rs1778477	HFE	cis	cerebellum	SCAN
rs1778477	AL022393.7	cis	Thyroid	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28235400-28249000	Weak transcription	Small Intestine	intestine
2	chr6:28235600-28249000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:28235600-28249000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:28236200-28249400	Weak transcription	Fetal Heart	heart
5	chr6:28237400-28249000	Weak transcription	Psoas Muscle	Psoas
6	chr6:28237600-28248800	Weak transcription	A549	lung
7	chr6:28238000-28248800	Weak transcription	Hela-S3	cervix
8	chr6:28240600-28248600	Weak transcription	HMEC	breast
9	chr6:28240600-28249000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:28241000-28249000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:28241200-28249000	Weak transcription	Colonic Mucosa	Colon
12	chr6:28241800-28249000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:28242000-28249000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:28242200-28249200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:28242400-28249000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:28242600-28249000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:28242600-28249000	Weak transcription	Fetal Intestine Small	intestine
18	chr6:28244400-28249400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:28244600-28249400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr6:28244800-28248600	Weak transcription	NHDF-Ad	bronchial
21	chr6:28244800-28248800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:28244800-28248800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr6:28244800-28248800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:28244800-28248800	Weak transcription	NH-A	brain
25	chr6:28245000-28248600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:28245000-28248800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:28245000-28248800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:28245000-28248800	Weak transcription	NHLF	lung
29	chr6:28245000-28249000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:28245000-28249000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:28245000-28249000	Weak transcription	Esophagus	oesophagus
32	chr6:28245000-28249000	Weak transcription	Fetal Kidney	kidney
33	chr6:28245000-28249000	Weak transcription	Gastric	stomach
34	chr6:28245000-28249000	Weak transcription	Pancreas	Pancrea
35	chr6:28245000-28249000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:28245000-28249000	Weak transcription	Thymus	Thymus
37	chr6:28245000-28249000	Weak transcription	NHEK	skin
38	chr6:28245000-28249400	Weak transcription	Spleen	Spleen
39	chr6:28245200-28248600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:28245200-28248600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:28245200-28248600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr6:28245200-28248600	Weak transcription	Adipose Nuclei	Adipose
43	chr6:28245200-28248600	Weak transcription	Brain Substantia Nigra	brain
44	chr6:28245200-28248600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr6:28245200-28248800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:28245200-28248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:28245200-28248800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr6:28245200-28248800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr6:28245200-28248800	Weak transcription	Brain Angular Gyrus	brain
50	chr6:28245200-28248800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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