Variant report

Variant	rs1778478
Chromosome Location	chr6:28247638-28247639
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28247522-28247825	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
2	chr6:28193103..28195771-chr6:28247213..28248961,2	K562	blood:
3	chr6:28246460..28249146-chr6:28271252..28274232,2	K562	blood:
4	chr6:28247415..28251168-chr6:28301808..28306623,8	K562	blood:
5	chr6:28186460..28191177-chr6:28246836..28252039,7	K562	blood:

No data

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

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1062169	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1119211	0.80[ASN][1000 genomes]
rs1150713	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150714	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	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1150720	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	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11757730	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11758337	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13210258	0.80[ASN][1000 genomes]
rs16893817	0.83[ASN][1000 genomes]
rs1778477	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185955	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2235359	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2281043	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800325	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56053755	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456811	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6456814	0.80[ASN][1000 genomes]
rs6923170	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1778478	AL022393.7	cis	Thyroid	GTEx

Chromatin state (count:119 , 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	chr6:28236200-28248000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:28236200-28249400	Weak transcription	Fetal Heart	heart
6	chr6:28237400-28249000	Weak transcription	Psoas Muscle	Psoas
7	chr6:28237600-28248800	Weak transcription	A549	lung
8	chr6:28238000-28248800	Weak transcription	Hela-S3	cervix
9	chr6:28240600-28248600	Weak transcription	HMEC	breast
10	chr6:28240600-28249000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:28241000-28249000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:28241200-28249000	Weak transcription	Colonic Mucosa	Colon
13	chr6:28241800-28249000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:28242000-28249000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:28242200-28249200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr6:28242400-28249000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:28242600-28249000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr6:28242600-28249000	Weak transcription	Fetal Intestine Small	intestine
19	chr6:28244400-28249400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:28244600-28249400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr6:28244800-28248400	Weak transcription	Dnd41	blood
22	chr6:28244800-28248600	Weak transcription	NHDF-Ad	bronchial
23	chr6:28244800-28248800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:28244800-28248800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr6:28244800-28248800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:28244800-28248800	Weak transcription	NH-A	brain
27	chr6:28245000-28248200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr6:28245000-28248600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:28245000-28248800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:28245000-28248800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:28245000-28248800	Weak transcription	NHLF	lung
32	chr6:28245000-28249000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:28245000-28249000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:28245000-28249000	Weak transcription	Esophagus	oesophagus
35	chr6:28245000-28249000	Weak transcription	Fetal Kidney	kidney
36	chr6:28245000-28249000	Weak transcription	Gastric	stomach
37	chr6:28245000-28249000	Weak transcription	Pancreas	Pancrea
38	chr6:28245000-28249000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:28245000-28249000	Weak transcription	Thymus	Thymus
40	chr6:28245000-28249000	Weak transcription	NHEK	skin
41	chr6:28245000-28249400	Weak transcription	Spleen	Spleen
42	chr6:28245200-28248000	Weak transcription	Fetal Thymus	thymus
43	chr6:28245200-28248600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr6:28245200-28248600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:28245200-28248600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:28245200-28248600	Weak transcription	Adipose Nuclei	Adipose
47	chr6:28245200-28248600	Weak transcription	Brain Substantia Nigra	brain
48	chr6:28245200-28248600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr6:28245200-28248800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:28245200-28248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links