Variant report

Variant	rs6798319
Chromosome Location	chr3:113631780-113631781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:113562771..113564177-chr3:113631595..113632434,6	MCF-7	breast:
2	chr3:113557327..113557954-chr3:113631676..113632377,2	MCF-7	breast:
3	chr3:113455391..113455958-chr3:113631755..113632390,2	MCF-7	breast:
4	chr3:113557477..113557996-chr3:113631505..113632468,2	MCF-7	breast:
5	chr3:113563225..113563984-chr3:113631500..113632478,4	K562	blood:
6	chr3:113557237..113558100-chr3:113631507..113632624,5	K562	blood:

Variant related genes	Relation type
ENSG00000178075	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17666485	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245830	0.81[JPT][hapmap]
rs2566973	0.82[JPT][hapmap]
rs2566976	0.82[JPT][hapmap]
rs2566977	0.82[JPT][hapmap]
rs4682143	0.82[JPT][hapmap]
rs6438172	0.82[JPT][hapmap]
rs72954636	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73230249	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv829678	chr3:113446177-113633053	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv877351	chr3:113450495-113637424	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1013746	chr3:113460162-113646657	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6798319	CD200R1L	cis	parietal	SCAN
rs6798319	ZNF80	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113618200-113641800	Weak transcription	Fetal Intestine Large	intestine
2	chr3:113619200-113652600	Weak transcription	Pancreas	Pancrea
3	chr3:113626200-113642200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:113626600-113641800	Weak transcription	Fetal Intestine Small	intestine
5	chr3:113629400-113633000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:113630400-113631800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:113631200-113632200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:113631400-113631800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr3:113631400-113632000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:113631400-113632000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:113631400-113632200	Enhancers	Primary B cells from peripheral blood	blood
12	chr3:113631400-113632200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:113631400-113632200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:113631400-113632200	Enhancers	Duodenum Mucosa	Duodenum
15	chr3:113631400-113632400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:113631400-113633600	Enhancers	Liver	Liver
17	chr3:113631600-113632000	Active TSS	Primary hematopoietic stem cells	blood
18	chr3:113631600-113632000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr3:113631600-113632000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:113631600-113632000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:113631600-113632000	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr3:113631600-113632000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr3:113631600-113632000	Enhancers	Dnd41	blood
24	chr3:113631600-113632000	Active TSS	GM12878-XiMat	blood
25	chr3:113631600-113632000	Enhancers	Hela-S3	cervix
26	chr3:113631600-113632000	Enhancers	NHEK	skin
27	chr3:113631600-113666200	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links