Variant report

Variant	rs2938691
Chromosome Location	chr15:76507206-76507207
allele	C/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	chr15:76506073..76507894-chr15:76510950..76513040,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1801591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1914816	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255408	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2456027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2456033	0.85[ASN][1000 genomes]
rs2456040	0.96[ASN][1000 genomes]
rs2456042	0.96[ASN][1000 genomes]
rs2456047	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2456051	0.81[CHD][hapmap]
rs2456053	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2456063	0.89[ASN][1000 genomes]
rs2456066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2456067	0.89[ASN][1000 genomes]
rs2456070	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2456072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2456074	0.96[ASN][1000 genomes]
rs2456075	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2456078	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460146	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460151	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460153	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs2460155	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2460158	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs2469211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2469212	0.86[ASN][1000 genomes]
rs2469214	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2469215	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2469216	0.85[ASN][1000 genomes]
rs2469533	0.82[ASN][1000 genomes]
rs2469538	0.96[ASN][1000 genomes]
rs2469539	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2469544	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2469552	0.85[ASN][1000 genomes]
rs2469559	0.81[CHD][hapmap]
rs2469564	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2469568	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2469573	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2956875	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2957037	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959846	0.96[ASN][1000 genomes]
rs4636879	0.82[GIH][hapmap];0.94[TSI][hapmap]
rs6495200	0.85[ASN][1000 genomes]
rs8042255	0.94[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2938691	PSTPIP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 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	chr15:76492000-76509600	Weak transcription	K562	blood
4	chr15:76492400-76510000	Strong transcription	Placenta	Placenta
5	chr15:76492800-76517600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:76492800-76526400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr15:76493200-76507800	Strong transcription	Fetal Stomach	stomach
8	chr15:76493600-76526400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:76494600-76510400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:76495400-76510400	Strong transcription	Adipose Nuclei	Adipose
11	chr15:76495800-76508600	Strong transcription	A549	lung
12	chr15:76496200-76510400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr15:76497000-76518200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr15:76497400-76509400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:76498200-76508800	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr15:76498200-76509200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:76498200-76510200	Strong transcription	Fetal Intestine Large	intestine
18	chr15:76498200-76511000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr15:76498200-76511600	Strong transcription	Primary T cells from cord blood	blood
20	chr15:76498400-76510600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr15:76498600-76510400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:76499200-76509000	Weak transcription	Stomach Mucosa	stomach
23	chr15:76499200-76509400	Weak transcription	Brain Germinal Matrix	brain
24	chr15:76499200-76509600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr15:76499200-76516800	Weak transcription	Brain Angular Gyrus	brain
26	chr15:76499200-76527400	Weak transcription	Fetal Brain Male	brain
27	chr15:76499800-76508200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:76499800-76509000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:76500000-76510400	Strong transcription	Liver	Liver
30	chr15:76500000-76510400	Strong transcription	Spleen	Spleen
31	chr15:76500200-76507800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:76500200-76508400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr15:76500200-76508400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr15:76500200-76510800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:76500400-76510400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr15:76500600-76508200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:76500600-76508200	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:76500600-76509600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr15:76500600-76534800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr15:76500800-76507600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:76500800-76508400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr15:76500800-76510400	Strong transcription	Fetal Intestine Small	intestine
43	chr15:76501000-76508400	Strong transcription	Lung	lung
44	chr15:76501000-76510400	Strong transcription	Fetal Muscle Leg	muscle
45	chr15:76501200-76508600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr15:76501200-76509600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr15:76501200-76524200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:76501400-76508200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr15:76501600-76508200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:76501600-76509200	Strong transcription	Dnd41	blood

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