Variant report

Variant	rs1869303
Chromosome Location	chr15:40804574-40804575
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40802752..40805307-chr15:40819242..40820883,2	K562	blood:
2	chr15:40789702..40793899-chr15:40802454..40805435,6	K562	blood:
3	chr15:40797459..40799431-chr15:40802673..40805643,2	K562	blood:
4	chr15:40730812..40733256-chr15:40803333..40806622,3	K562	blood:
5	chr15:40762122..40764569-chr15:40802898..40805797,2	MCF-7	breast:
6	chr15:40730812..40737363-chr15:40801226..40806622,9	K562	blood:
7	chr15:40800305..40802269-chr15:40802285..40805070,2	K562	blood:

Variant related genes	Relation type
ENSG00000169105	Chromatin interaction
ENSG00000140320	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10444792	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10518696	1.00[CEU][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10851397	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11070276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070278	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11632319	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12442697	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12916218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1453182	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1530942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1530943	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16970734	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16970854	1.00[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1801320	1.00[CEU][hapmap]
rs1987795	0.91[AMR][1000 genomes]
rs2014367	1.00[CEU][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2034653	0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2084941	0.85[EUR][1000 genomes]
rs2278887	0.86[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap]
rs2278889	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2290379	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2304579	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap]
rs2412528	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412530	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2412533	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2924389	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2959535	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2959547	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3803354	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4467046	0.88[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4561439	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4923873	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4923877	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.84[LWK][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4923878	1.00[CEU][hapmap];0.94[GIH][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4923879	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4924473	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924476	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924482	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4924483	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57140606	0.89[EUR][1000 genomes]
rs57736474	0.87[EUR][1000 genomes]
rs582736	0.87[CEU][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs589650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs607118	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs611933	0.87[CEU][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs617031	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs623187	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs624486	0.87[CEU][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs640919	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6492952	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6492953	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6492955	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs651131	0.84[EUR][1000 genomes]
rs667623	0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs7163648	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7163889	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7164056	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7164166	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7164405	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7167239	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7167922	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7168913	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7168927	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7169872	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7170073	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7170327	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7170946	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73396510	0.87[EUR][1000 genomes]
rs73396515	0.87[EUR][1000 genomes]
rs8024579	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8024802	1.00[CEU][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8029208	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8032453	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8033739	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8034726	1.00[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8038350	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8040187	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];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8041816	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8041991	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8043197	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs896797	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs921624	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9284288	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs976402	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9783737	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1869303	MRPL42P5	cis	multi-tissue	Pritchard
rs1869303	C15orf57	cis	Whole Blood	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40803200-40804600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr15:40803200-40804600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:40803200-40804600	Active TSS	Rectal Smooth Muscle	rectum
4	chr15:40803200-40804600	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr15:40803400-40804600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
6	chr15:40803600-40804600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
7	chr15:40803600-40804600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:40803600-40804600	Active TSS	Brain Anterior Caudate	brain
9	chr15:40803600-40804600	Active TSS	Colon Smooth Muscle	Colon
10	chr15:40803600-40804600	Flanking Active TSS	Hela-S3	cervix
11	chr15:40803600-40804800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr15:40803800-40804600	Bivalent Enhancer	Fetal Thymus	thymus
13	chr15:40803800-40804600	Active TSS	A549	lung
14	chr15:40804000-40804600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:40804000-40804600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
16	chr15:40804000-40804600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr15:40804000-40804600	Enhancers	Small Intestine	intestine
18	chr15:40804000-40804600	Flanking Active TSS	K562	blood
19	chr15:40804200-40804600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:40804200-40804600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:40804200-40804600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:40804200-40804600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:40804200-40804600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
24	chr15:40804200-40804600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr15:40804200-40804600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
26	chr15:40804200-40804600	Enhancers	Placenta Amnion	Placenta Amnion
27	chr15:40804200-40804600	Flanking Bivalent TSS/Enh	HepG2	liver
28	chr15:40804200-40804800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:40804200-40804800	Enhancers	GM12878-XiMat	blood
30	chr15:40804200-40807600	Weak transcription	NHDF-Ad	bronchial
31	chr15:40804400-40804600	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
32	chr15:40804400-40804600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
33	chr15:40804400-40804600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
34	chr15:40804400-40804600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr15:40804400-40804600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:40804400-40804600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:40804400-40804600	Enhancers	Adipose Nuclei	Adipose
38	chr15:40804400-40804600	Enhancers	Liver	Liver
39	chr15:40804400-40804600	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr15:40804400-40804600	Enhancers	Brain Cingulate Gyrus	brain
41	chr15:40804400-40804600	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr15:40804400-40804600	Enhancers	Brain Substantia Nigra	brain
43	chr15:40804400-40804600	Enhancers	Colonic Mucosa	Colon
44	chr15:40804400-40804600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr15:40804400-40804600	Bivalent Enhancer	Fetal Intestine Large	intestine
46	chr15:40804400-40804600	Bivalent Enhancer	Fetal Intestine Small	intestine
47	chr15:40804400-40804600	Enhancers	Fetal Lung	lung
48	chr15:40804400-40804600	Enhancers	Left Ventricle	heart
49	chr15:40804400-40804600	Enhancers	Ovary	ovary
50	chr15:40804400-40804600	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links