Variant report

Variant	rs2255408
Chromosome Location	chr15:76503295-76503296
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:76503018..76504936-chr15:76506682..76510491,3	MCF-7	breast:
2	chr15:76487953..76490483-chr15:76500123..76503783,3	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1801591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1914816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2456027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2456040	0.85[ASN][1000 genomes]
rs2456042	0.85[ASN][1000 genomes]
rs2456047	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2456051	0.81[CHD][hapmap]
rs2456053	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2456066	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2456070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2456072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2456074	0.85[ASN][1000 genomes]
rs2456075	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2456078	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2460146	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2460151	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2460153	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2460155	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2460158	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2469211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs2469214	0.82[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2469215	1.00[CHB][hapmap]
rs2469538	0.85[ASN][1000 genomes]
rs2469539	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2469544	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2469559	0.81[CHD][hapmap]
rs2469564	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2469568	1.00[CHB][hapmap]
rs2469573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs2938691	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2956875	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2957037	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2959846	0.85[ASN][1000 genomes]
rs4636879	0.91[TSI][hapmap]
rs8042255	0.88[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

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	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv833057	chr15:76367848-76585868	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1054713	chr15:76460462-76505906	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2255408	PSTPIP1	cis	lymphoblastoid	seeQTL
rs2255408	ISL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76486800-76516600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr15:76489400-76519800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:76490000-76503600	Weak transcription	HUVEC	blood vessel
4	chr15:76492000-76503600	Weak transcription	NHDF-Ad	bronchial
5	chr15:76492000-76509600	Weak transcription	K562	blood
6	chr15:76492400-76510000	Strong transcription	Placenta	Placenta
7	chr15:76492600-76507000	Weak transcription	NH-A	brain
8	chr15:76492800-76506200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:76492800-76517600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr15:76492800-76526400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:76493000-76504200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:76493200-76507800	Strong transcription	Fetal Stomach	stomach
13	chr15:76493400-76504400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:76493600-76506800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:76493600-76526400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr15:76494600-76510400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:76495400-76510400	Strong transcription	Adipose Nuclei	Adipose
18	chr15:76495800-76508600	Strong transcription	A549	lung
19	chr15:76496200-76510400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:76497000-76518200	Strong transcription	Duodenum Mucosa	Duodenum
21	chr15:76497400-76509400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:76497600-76505600	Weak transcription	Ovary	ovary
23	chr15:76498200-76506400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:76498200-76508800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr15:76498200-76509200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:76498200-76510200	Strong transcription	Fetal Intestine Large	intestine
27	chr15:76498200-76511000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr15:76498200-76511600	Strong transcription	Primary T cells from cord blood	blood
29	chr15:76498400-76510600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr15:76498600-76506000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr15:76498600-76510400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:76499200-76503800	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:76499200-76504000	Weak transcription	Brain Substantia Nigra	brain
34	chr15:76499200-76506800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr15:76499200-76509000	Weak transcription	Stomach Mucosa	stomach
36	chr15:76499200-76509400	Weak transcription	Brain Germinal Matrix	brain
37	chr15:76499200-76509600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:76499200-76516800	Weak transcription	Brain Angular Gyrus	brain
39	chr15:76499200-76527400	Weak transcription	Fetal Brain Male	brain
40	chr15:76499800-76508200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr15:76499800-76509000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:76500000-76510400	Strong transcription	Liver	Liver
43	chr15:76500000-76510400	Strong transcription	Spleen	Spleen
44	chr15:76500200-76505000	Strong transcription	Primary hematopoietic stem cells	blood
45	chr15:76500200-76507800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:76500200-76508400	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr15:76500200-76508400	Strong transcription	Stomach Smooth Muscle	stomach
48	chr15:76500200-76510800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:76500400-76510400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr15:76500600-76508200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links