Variant report

Variant	rs6708927
Chromosome Location	chr2:113244960-113244961
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113238709..113241240-chr2:113244308..113247032,3	MCF-7	breast:
2	chr2:113243489..113245525-chr2:113319598..113322225,2	K562	blood:
3	chr2:113244108..113246040-chr2:113250094..113252962,3	MCF-7	breast:
4	chr2:113244367..113247347-chr2:113249127..113251092,3	MCF-7	breast:
5	chr2:113239427..113241557-chr2:113241799..113245062,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114999	Chromatin interaction
ENSG00000125630	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11679929	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987434	1.00[ASN][1000 genomes]
rs12988536	1.00[ASN][1000 genomes]
rs12989407	1.00[ASN][1000 genomes]
rs13025468	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs1465817	0.93[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561266	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs34047777	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34263686	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34364366	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34892661	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36086865	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3961916	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs62158651	1.00[ASN][1000 genomes]
rs6707618	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6708841	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67178025	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726169	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729910	0.85[CEU][hapmap]
rs6759275	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs71414672	1.00[ASN][1000 genomes]
rs71414673	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570679	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573493	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586685	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589793	0.86[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	nsv949573	chr2:112986955-113320975	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6708927	RGPD8	cis	lung	GTEx
rs6708927	RGPD8	cis	Muscle Skeletal	GTEx
rs6708927	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs6708927	RGPD8	cis	Esophagus Mucosa	GTEx
rs6708927	RGPD8	cis	Adipose Subcutaneous	GTEx
rs6708927	RGPD8	cis	Artery Aorta	GTEx
rs6708927	RGPD8	cis	Artery Tibial	GTEx
rs6708927	RGPD8	cis	Nerve Tibial	GTEx
rs6708927	RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL
rs6708927	RGPD8	cis	Whole Blood	GTEx
rs6708927	RGPD8	cis	Thyroid	GTEx
rs6708927	RGPD8	cis	Esophagus Muscularis	GTEx
rs6708927	RGPD8	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113240800-113251600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:113241000-113250600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:113241000-113251600	Weak transcription	Aorta	Aorta
4	chr2:113241000-113277200	Weak transcription	Gastric	stomach
5	chr2:113241000-113277800	Weak transcription	Colonic Mucosa	Colon
6	chr2:113241200-113251000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:113241200-113251600	Weak transcription	Placenta	Placenta
8	chr2:113241200-113251800	Weak transcription	Left Ventricle	heart
9	chr2:113241200-113251800	Weak transcription	Psoas Muscle	Psoas
10	chr2:113241200-113252200	Weak transcription	Ovary	ovary
11	chr2:113241200-113259600	Weak transcription	Esophagus	oesophagus
12	chr2:113241200-113271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:113241200-113277800	Weak transcription	Pancreas	Pancrea
14	chr2:113241200-113278000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:113241200-113286400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:113241400-113251000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:113241400-113251600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:113241400-113251800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:113241400-113252000	Weak transcription	Fetal Kidney	kidney
20	chr2:113241400-113254000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:113241400-113279200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:113241600-113245200	Weak transcription	Right Ventricle	heart
23	chr2:113241600-113250800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:113241600-113250800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:113241600-113251600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:113241600-113251600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:113241600-113251600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:113241600-113251800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:113241600-113252000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:113241600-113252600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:113241600-113260600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr2:113241600-113277200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:113241600-113292400	Weak transcription	Small Intestine	intestine
34	chr2:113241800-113245200	Weak transcription	Adipose Nuclei	Adipose
35	chr2:113241800-113245200	Weak transcription	Right Atrium	heart
36	chr2:113241800-113245600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:113241800-113246000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:113241800-113246400	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:113241800-113250600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:113241800-113250600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:113241800-113250800	Weak transcription	Stomach Mucosa	stomach
42	chr2:113241800-113251000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:113241800-113251000	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr2:113241800-113251400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:113241800-113251400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:113241800-113251600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:113241800-113251600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:113241800-113251800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr2:113241800-113251800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:113241800-113252000	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links