Variant report

Variant	rs4886799
Chromosome Location	chr15:76677241-76677242
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76670479..76673232-chr15:76675468..76677243,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs11072580	0.88[JPT][hapmap]
rs11072599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1117367	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1125932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12148786	0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs12148805	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12437627	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs12438077	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12439484	0.83[JPT][hapmap]
rs12440815	0.86[ASN][1000 genomes]
rs12441433	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs12441550	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12442266	0.82[JPT][hapmap]
rs12443137	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12592171	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12592386	0.90[ASN][1000 genomes]
rs12592420	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12593751	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12594577	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12898415	0.88[JPT][hapmap]
rs12899871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12902174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12902414	0.87[ASN][1000 genomes]
rs12907668	0.82[JPT][hapmap]
rs12907805	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12908334	0.88[JPT][hapmap]
rs12913096	0.83[JPT][hapmap]
rs12914005	0.84[ASN][1000 genomes]
rs12915248	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12916573	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12917430	1.00[ASN][1000 genomes]
rs1587381	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1588961	0.84[ASN][1000 genomes]
rs17361504	0.83[JPT][hapmap]
rs17362383	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17363713	0.86[ASN][1000 genomes]
rs17364076	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17364330	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17460201	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17461634	0.84[ASN][1000 genomes]
rs1874944	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1875884	0.95[ASN][1000 genomes]
rs1875885	0.95[ASN][1000 genomes]
rs1965492	0.81[ASN][1000 genomes]
rs2117369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2120107	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs2120108	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs2164101	0.84[ASN][1000 genomes]
rs2176623	0.83[JPT][hapmap]
rs2404740	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2469542	0.88[JPT][hapmap]
rs284895	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3759853	0.83[JPT][hapmap]
rs3866543	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs4079681	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4633676	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4886496	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4886801	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886813	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs56089215	0.87[ASN][1000 genomes]
rs56216512	0.92[ASN][1000 genomes]
rs58684938	0.98[ASN][1000 genomes]
rs66986092	0.87[ASN][1000 genomes]
rs67232575	0.83[ASN][1000 genomes]
rs67263359	0.87[ASN][1000 genomes]
rs67418609	0.86[ASN][1000 genomes]
rs67888330	0.86[ASN][1000 genomes]
rs67920045	0.86[ASN][1000 genomes]
rs7162455	0.81[ASN][1000 genomes]
rs7163946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7164060	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7164813	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7165025	0.84[ASN][1000 genomes]
rs7179142	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7403276	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8025134	0.84[ASN][1000 genomes]
rs8030411	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8039545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][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	nsv510667	chr15:76653359-76708310	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4886799	NRG4	cis	parietal	SCAN
rs4886799	SCAPER	cis	cerebellum	SCAN
rs4886799	SCAPER	cis	parietal	SCAN
rs4886799	C15orf17	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76639800-76682600	Weak transcription	Pancreas	Pancrea
2	chr15:76639800-76695400	Weak transcription	Spleen	Spleen
3	chr15:76639800-76727400	Weak transcription	Right Ventricle	heart
4	chr15:76640800-76694600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr15:76641400-76694600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:76642800-76693800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr15:76643800-76695000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:76645800-76686200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:76646600-76695400	Weak transcription	Ovary	ovary
10	chr15:76660800-76693600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:76661000-76685800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:76661000-76695200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:76661000-76695400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr15:76661000-76695400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:76661000-76708600	Weak transcription	Brain Anterior Caudate	brain
16	chr15:76661200-76698000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr15:76661200-76710800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:76661600-76698000	Weak transcription	Dnd41	blood
19	chr15:76662400-76679000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr15:76662400-76695400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:76662800-76679200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr15:76664800-76698000	Weak transcription	Brain Hippocampus Middle	brain
23	chr15:76666200-76679400	Weak transcription	Placenta	Placenta
24	chr15:76666200-76694600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:76666200-76696200	Weak transcription	Brain Angular Gyrus	brain
26	chr15:76666200-76706800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr15:76666400-76694600	Weak transcription	Adipose Nuclei	Adipose
28	chr15:76666400-76695200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr15:76666400-76695400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:76666400-76698200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr15:76666600-76695200	Weak transcription	Fetal Muscle Leg	muscle
32	chr15:76667200-76681600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr15:76668800-76679600	Weak transcription	Thymus	Thymus
34	chr15:76668800-76695000	Weak transcription	Fetal Brain Female	brain
35	chr15:76668800-76695400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr15:76669600-76695200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr15:76669800-76693600	Weak transcription	Fetal Intestine Large	intestine
38	chr15:76669800-76694200	Weak transcription	Psoas Muscle	Psoas
39	chr15:76670600-76677600	Weak transcription	Liver	Liver
40	chr15:76670600-76683400	Weak transcription	HepG2	liver
41	chr15:76673200-76686000	Weak transcription	Fetal Stomach	stomach
42	chr15:76673200-76727400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:76673800-76694800	Weak transcription	Primary B cells from cord blood	blood
44	chr15:76674000-76682000	Weak transcription	Fetal Intestine Small	intestine
45	chr15:76674400-76695400	Weak transcription	Lung	lung
46	chr15:76674600-76677600	Weak transcription	Left Ventricle	heart
47	chr15:76674600-76680800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:76674600-76694800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr15:76674600-76718400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:76675200-76677600	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links