Variant report

Variant	rs693919
Chromosome Location	chr15:44102328-44102329
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	chr15:44067455..44069837-chr15:44100088..44102912,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140264	Chromatin interaction
ENSG00000128886	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10163054	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10438303	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs1053492	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11070408	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs11070410	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11070412	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11638972	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11852840	0.92[ASN][1000 genomes]
rs11856495	0.91[ASN][1000 genomes]
rs11856795	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs12101756	0.84[ASN][1000 genomes]
rs12440573	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12441127	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12441861	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12441984	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12442129	0.87[ASN][1000 genomes]
rs12443102	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs12702	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12899922	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12908467	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13380397	0.88[ASN][1000 genomes]
rs16950562	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs16963953	0.95[ASN][1000 genomes]
rs16965120	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16977724	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs16977798	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1965794	0.87[ASN][1000 genomes]
rs1965795	0.94[ASN][1000 genomes]
rs1975364	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2228368	1.00[ASN][1000 genomes]
rs2277531	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2411284	0.83[EUR][1000 genomes]
rs2412823	0.82[CEU][hapmap]
rs2447193	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2447208	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs2467402	0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs2470121	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2614811	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2788	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs28377539	0.87[ASN][1000 genomes]
rs28413704	0.94[ASN][1000 genomes]
rs28476182	0.94[ASN][1000 genomes]
rs28509275	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs28513374	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs28519630	0.94[ASN][1000 genomes]
rs28524541	0.95[ASN][1000 genomes]
rs28531819	0.95[ASN][1000 genomes]
rs28546844	0.90[ASN][1000 genomes]
rs28564774	0.95[ASN][1000 genomes]
rs28578398	0.93[ASN][1000 genomes]
rs28583806	1.00[ASN][1000 genomes]
rs28590651	0.98[ASN][1000 genomes]
rs28595038	0.85[ASN][1000 genomes]
rs28636829	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28674750	0.98[ASN][1000 genomes]
rs28678901	0.94[ASN][1000 genomes]
rs28679673	0.95[ASN][1000 genomes]
rs28684672	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28687459	0.95[ASN][1000 genomes]
rs28696802	0.95[ASN][1000 genomes]
rs28707214	0.95[ASN][1000 genomes]
rs28718261	0.85[ASN][1000 genomes]
rs28780699	0.95[ASN][1000 genomes]
rs28781888	0.95[ASN][1000 genomes]
rs28823973	0.86[ASN][1000 genomes]
rs28858500	0.85[ASN][1000 genomes]
rs28866846	0.93[ASN][1000 genomes]
rs28891769	0.93[ASN][1000 genomes]
rs2920781	0.90[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs2927071	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2927072	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2927085	0.86[CEU][hapmap]
rs2955969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3087657	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3101443	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs35866764	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3736180	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3742982	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs3759790	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs3759791	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3816792	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs3825783	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3862142	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap]
rs4332723	0.86[EUR][1000 genomes]
rs4617832	0.83[EUR][1000 genomes]
rs4924722	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4997480	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs524908	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs533143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap]
rs56008017	0.94[ASN][1000 genomes]
rs56909447	0.95[ASN][1000 genomes]
rs575082	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60883262	0.94[ASN][1000 genomes]
rs61390361	0.83[ASN][1000 genomes]
rs62018947	0.83[EUR][1000 genomes]
rs62018952	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs663214	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs667476	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs68079546	0.95[ASN][1000 genomes]
rs686666	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs688009	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs694461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168158	0.85[ASN][1000 genomes]
rs7169322	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7169382	1.00[ASN][1000 genomes]
rs7169988	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs7170167	0.86[ASN][1000 genomes]
rs7170751	0.88[ASN][1000 genomes]
rs7171750	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7174208	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7175032	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7175129	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs7178343	0.83[EUR][1000 genomes]
rs7179388	0.95[ASN][1000 genomes]
rs7180818	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7183809	0.95[ASN][1000 genomes]
rs8023458	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs8023508	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs8032649	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs8034451	0.82[EUR][1000 genomes]
rs8040839	0.97[ASN][1000 genomes]
rs8042868	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap]
rs9944216	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs9989313	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
9	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
10	nsv1036318	chr15:44053617-44160773	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	nsv1050263	chr15:44093927-44204047	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs693919	STRCP1	cis	Whole Blood	GTEx
rs693919	WDR76	cis	parietal	SCAN
rs693919	ZNF690	cis	multi-tissue	Pritchard
rs693919	ELL3	cis	multi-tissue	Pritchard
rs693919	ZSCAN29	cis	Thyroid	GTEx
rs693919	STRC	cis	multi-tissue	Pritchard
rs693919	ADAL	cis	parietal	SCAN
rs693919	DUOX2	cis	parietal	SCAN
rs693919	STRCP1	cis	Thyroid	GTEx
rs693919	AC011330.5	cis	Artery Tibial	GTEx
rs693919	AC011330.5	cis	Thyroid	GTEx
rs693919	PATL2	cis	cerebellum	SCAN
rs693919	SERF2	cis	lymphoblastoid	seeQTL
rs693919	TGM5	cis	lymphoblastoid	seeQTL
rs693919	C15orf43	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44093600-44103400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:44093600-44116000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:44093600-44116400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:44093800-44105400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:44093800-44107000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:44093800-44109000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:44093800-44112800	Strong transcription	Thymus	Thymus
8	chr15:44093800-44113800	Weak transcription	Stomach Mucosa	stomach
9	chr15:44093800-44115800	Weak transcription	Right Atrium	heart
10	chr15:44094000-44107800	Strong transcription	Lung	lung
11	chr15:44094000-44109800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:44094000-44110000	Strong transcription	Brain Anterior Caudate	brain
13	chr15:44094000-44110000	Strong transcription	Placenta	Placenta
14	chr15:44094000-44110000	Strong transcription	Fetal Thymus	thymus
15	chr15:44094000-44110000	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:44094000-44110000	Strong transcription	Stomach Smooth Muscle	stomach
17	chr15:44094000-44110200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:44094000-44110200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr15:44094000-44110200	Strong transcription	Fetal Intestine Large	intestine
20	chr15:44094000-44110400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:44094000-44110400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:44094000-44110800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr15:44094000-44111200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:44094000-44111200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr15:44094000-44113200	Strong transcription	Fetal Muscle Leg	muscle
26	chr15:44094000-44113400	Strong transcription	Fetal Stomach	stomach
27	chr15:44094000-44114600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:44094000-44114800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:44094200-44108000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:44094200-44110000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:44094200-44110000	Strong transcription	Adipose Nuclei	Adipose
32	chr15:44094200-44110000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr15:44094200-44110200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr15:44094200-44110200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:44094200-44110200	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:44094200-44110600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:44094200-44111200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr15:44094200-44111200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:44094200-44111400	Strong transcription	Primary T cells from cord blood	blood
40	chr15:44094200-44111600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:44094200-44113000	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr15:44094200-44113200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:44094400-44102400	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr15:44094400-44107400	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr15:44094400-44109800	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr15:44094400-44110000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:44094400-44110000	Strong transcription	Dnd41	blood
48	chr15:44094400-44110200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:44094400-44110200	Strong transcription	Liver	Liver
50	chr15:44094400-44110400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links