Variant report

Variant	rs8041902
Chromosome Location	chr15:45878015-45878016
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr15:45878015-45880689	H1-neurons	neurons:	n/a	chr15:45879843-45879863
2	POLR2A	chr15:45877993-45878510	MCF-7	breast:	n/a	n/a
3	POLR2A	chr15:45877418-45881150	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45877501..45879866-chr15:45923125..45926614,3	MCF-7	breast:
2	chr15:45813492..45816353-chr15:45876550..45880712,4	MCF-7	breast:
3	chr15:45855963..45859182-chr15:45877803..45880512,3	MCF-7	breast:
4	chr15:45877908..45881944-chr15:45926466..45928753,3	MCF-7	breast:
5	chr15:45693513..45696404-chr15:45876472..45881031,4	MCF-7	breast:

Variant related genes	Relation type
BLOC1S6	TF binding region
ENSG00000260170	TF binding region
ENSG00000171766	Chromatin interaction
ENSG00000137767	Chromatin interaction
ENSG00000259427	Chromatin interaction
ENSG00000104154	Chromatin interaction
ENSG00000179362	Chromatin interaction
ENSG00000171763	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11632553	0.83[CEU][hapmap]
rs11637984	0.83[CEU][hapmap]
rs16945097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16946621	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs17627219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1966763	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2083728	1.00[CEU][hapmap]
rs55755923	0.90[EUR][1000 genomes]
rs55806911	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55913172	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55997350	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56081351	0.91[EUR][1000 genomes]
rs56179992	0.84[ASN][1000 genomes]
rs56190351	0.91[EUR][1000 genomes]
rs56259807	0.91[EUR][1000 genomes]
rs56304405	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56375332	0.91[EUR][1000 genomes]
rs56395216	0.91[EUR][1000 genomes]
rs57291883	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59593563	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60351453	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60378269	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60992352	0.84[ASN][1000 genomes]
rs61209164	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68044128	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs685812	1.00[CEU][hapmap]
rs7164956	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7165827	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7169748	1.00[JPT][hapmap]
rs7170090	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7175288	0.94[CEU][hapmap]
rs7178395	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178879	1.00[ASN][1000 genomes]
rs7179265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179903	1.00[ASN][1000 genomes]
rs7181436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72711301	0.84[ASN][1000 genomes]
rs72713103	0.84[ASN][1000 genomes]
rs72713104	0.84[ASN][1000 genomes]
rs72713105	0.84[ASN][1000 genomes]
rs72713106	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713107	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713168	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713169	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713171	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713172	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713175	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72713177	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72713178	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72713180	0.80[EUR][1000 genomes]
rs72713182	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72713185	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72713191	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72713197	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72713199	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72713201	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72715003	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72715005	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72715008	0.90[EUR][1000 genomes]
rs72715010	0.91[EUR][1000 genomes]
rs72715014	0.91[EUR][1000 genomes]
rs72715019	0.91[EUR][1000 genomes]
rs72715020	0.91[EUR][1000 genomes]
rs72715077	0.91[EUR][1000 genomes]
rs8025407	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs8039784	0.83[CEU][hapmap]
rs8043334	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045556	chr15:45777396-45884854	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv904188	chr15:45801035-45941689	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs8041902	TMEM62	cis	cerebellum	SCAN
rs8041902	MGA	cis	parietal	SCAN
rs8041902	GPR176	cis	cerebellum	SCAN
rs8041902	RPAP1	cis	cerebellum	SCAN
rs8041902	SLC30A4	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45875400-45878600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr15:45876200-45878200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr15:45876400-45878800	Weak transcription	Aorta	Aorta
4	chr15:45876800-45878400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:45876800-45878400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr15:45876800-45878600	Enhancers	Placenta	Placenta
7	chr15:45877200-45878400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:45877400-45878200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr15:45877400-45878200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:45877400-45878200	Enhancers	Fetal Lung	lung
11	chr15:45877400-45878400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr15:45877400-45878400	Enhancers	Fetal Intestine Large	intestine
13	chr15:45877400-45878600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr15:45877400-45878600	Enhancers	Fetal Muscle Leg	muscle
15	chr15:45877400-45878800	Enhancers	Placenta Amnion	Placenta Amnion
16	chr15:45877400-45881800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:45877600-45878200	Active TSS	GM12878-XiMat	blood
18	chr15:45877600-45878400	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr15:45877600-45878400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr15:45877600-45878400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:45877600-45878600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr15:45877600-45878600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr15:45877800-45878200	Enhancers	Primary B cells from cord blood	blood
24	chr15:45877800-45878200	Enhancers	Primary T cells from cord blood	blood
25	chr15:45877800-45878200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:45877800-45878200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:45877800-45878200	Enhancers	Brain Hippocampus Middle	brain
28	chr15:45877800-45878200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:45877800-45878200	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr15:45877800-45878600	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr15:45877800-45878800	Enhancers	Fetal Heart	heart
32	chr15:45878000-45878200	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr15:45878000-45878200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr15:45878000-45878200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:45878000-45878200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:45878000-45878200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:45878000-45878200	Enhancers	Adipose Nuclei	Adipose
38	chr15:45878000-45878200	Enhancers	Brain Substantia Nigra	brain
39	chr15:45878000-45878200	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr15:45878000-45878200	Flanking Active TSS	Fetal Brain Female	brain
41	chr15:45878000-45878200	Enhancers	Fetal Intestine Small	intestine
42	chr15:45878000-45878200	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr15:45878000-45878200	Enhancers	Rectal Smooth Muscle	rectum
44	chr15:45878000-45878200	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr15:45878000-45878200	Enhancers	Hela-S3	cervix
46	chr15:45878000-45878200	Enhancers	HMEC	breast
47	chr15:45878000-45878200	Enhancers	NHEK	skin
48	chr15:45878000-45878400	Enhancers	Primary hematopoietic stem cells	blood
49	chr15:45878000-45878400	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr15:45878000-45878400	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links