Variant report

Variant	rs2535260
Chromosome Location	chr6:29628883-29628884
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1122947	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1984840	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2079898	0.81[ASN][1000 genomes]
rs2262263	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2535245	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2535246	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2747453	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2747455	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs29231	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs29273	0.97[ASN][1000 genomes]
rs2982837	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3095287	0.81[ASN][1000 genomes]
rs3129074	0.81[ASN][1000 genomes]
rs3129087	0.81[ASN][1000 genomes]
rs3129090	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3131879	0.81[ASN][1000 genomes]
rs3131881	0.81[ASN][1000 genomes]
rs3131882	0.81[ASN][1000 genomes]
rs6941117	0.81[ASN][1000 genomes]
rs7774576	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7776296	0.81[ASN][1000 genomes]
rs9257931	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9258094	0.81[ASN][1000 genomes]
rs9258102	0.81[ASN][1000 genomes]
rs9258114	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2535260	HLA-A	cis	multi-tissue	Pritchard
rs2535260	BTN3A1	cis	parietal	SCAN
rs2535260	HLA-H	cis	multi-tissue	Pritchard

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29618400-29629000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:29618400-29629600	Weak transcription	Right Ventricle	heart
3	chr6:29620000-29631200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:29623400-29630600	Active TSS	Brain Anterior Caudate	brain
5	chr6:29624400-29629200	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr6:29624400-29630400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:29624800-29629000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:29624800-29631600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:29625000-29629000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:29625000-29629200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
12	chr6:29626600-29631400	Weak transcription	Fetal Heart	heart
13	chr6:29627800-29629600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:29628000-29630200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:29628400-29630200	Active TSS	Brain Hippocampus Middle	brain
16	chr6:29628600-29629000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr6:29628600-29631800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr6:29628600-29632000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr6:29628800-29629000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr6:29628800-29629000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr6:29628800-29629200	Enhancers	H1 Cell Line	embryonic stem cell
22	chr6:29628800-29629200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:29628800-29629400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr6:29628800-29629400	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr6:29628800-29629600	Active TSS	Brain Angular Gyrus	brain
26	chr6:29628800-29629600	Active TSS	Brain Cingulate Gyrus	brain
27	chr6:29628800-29629600	Active TSS	Brain Substantia Nigra	brain
28	chr6:29628800-29631600	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links