Variant report

Variant	rs12923
Chromosome Location	chr15:50570036-50570037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50563105..50566724-chr15:50567713..50571020,4	K562	blood:
2	chr15:50563105..50565839-chr15:50567791..50570281,2	K562	blood:
3	chr15:50559504..50561067-chr15:50567809..50570782,2	K562	blood:
4	chr15:50559536..50561689-chr15:50567895..50570297,2	K562	blood:
5	chr15:50489080..50491819-chr15:50568485..50571202,2	K562	blood:
6	chr15:50569600..50571427-chr15:50584025..50585795,2	K562	blood:
7	chr15:50567008..50568947-chr15:50569123..50571870,2	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs11070766	0.87[ASN][1000 genomes]
rs11070768	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11629603	0.91[ASN][1000 genomes]
rs11630045	0.92[ASN][1000 genomes]
rs11630063	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11631197	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11631985	0.91[ASN][1000 genomes]
rs11632019	0.87[ASN][1000 genomes]
rs11632703	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[ASN][1000 genomes]
rs11635546	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs11636564	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[ASN][1000 genomes]
rs11636908	0.89[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11637901	0.91[ASN][1000 genomes]
rs11637975	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11638432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11638564	0.91[ASN][1000 genomes]
rs11639406	1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11852487	1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[ASN][1000 genomes]
rs11853236	0.87[ASN][1000 genomes]
rs11855823	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12440811	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs12902318	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[ASN][1000 genomes]
rs12904469	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12906304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908591	1.00[ASW][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12909337	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12910368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910586	0.87[ASN][1000 genomes]
rs12912679	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12912969	0.91[ASN][1000 genomes]
rs1645	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16963604	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16963612	0.87[ASN][1000 genomes]
rs17508371	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[ASN][1000 genomes]
rs17509944	1.00[JPT][hapmap]
rs1972700	0.83[ASN][1000 genomes]
rs2033115	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2081628	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[ASN][1000 genomes]
rs28372114	0.87[ASN][1000 genomes]
rs28408662	0.91[ASN][1000 genomes]
rs28451583	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28453939	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28531946	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28534445	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28609286	0.87[ASN][1000 genomes]
rs28669213	0.92[ASN][1000 genomes]
rs28688566	0.91[ASN][1000 genomes]
rs28690939	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28715646	0.91[ASN][1000 genomes]
rs28716586	0.91[ASN][1000 genomes]
rs28719982	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34143694	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34197276	0.87[ASN][1000 genomes]
rs34312018	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34405772	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34590486	0.91[ASN][1000 genomes]
rs35000991	0.91[ASN][1000 genomes]
rs35013067	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35024305	0.87[ASN][1000 genomes]
rs35033384	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35168369	0.91[ASN][1000 genomes]
rs35354250	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35446819	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs35453213	0.95[ASN][1000 genomes]
rs4774559	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4775872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775873	1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4775874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4775875	0.87[ASN][1000 genomes]
rs4775876	1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[ASN][1000 genomes]
rs4775877	0.91[ASN][1000 genomes]
rs493971	0.86[LWK][hapmap]
rs526045	1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs526952	1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62022571	0.80[ASN][1000 genomes]
rs6493429	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7163457	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[ASN][1000 genomes]
rs7164375	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7164377	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7164798	1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7173127	1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7175150	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7176792	0.96[ASN][1000 genomes]
rs7183422	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73399285	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8024514	1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8025367	0.91[ASN][1000 genomes]
rs8026571	0.91[ASN][1000 genomes]
rs8027367	0.91[ASN][1000 genomes]
rs8030952	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8034597	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034615	0.91[ASN][1000 genomes]
rs8036354	1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs8042053	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8043475	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50555400-50579400	Weak transcription	K562	blood
2	chr15:50558000-50572400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:50564000-50574400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:50564200-50572400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:50566000-50576200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr15:50566000-50580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr15:50566400-50576400	Weak transcription	HUVEC	blood vessel
8	chr15:50566600-50572000	Weak transcription	NHEK	skin
9	chr15:50567200-50576200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:50567200-50579600	Weak transcription	Fetal Brain Female	brain
11	chr15:50567200-50579600	Weak transcription	Left Ventricle	heart
12	chr15:50567200-50579600	Weak transcription	Ovary	ovary
13	chr15:50567200-50580000	Weak transcription	Brain Germinal Matrix	brain
14	chr15:50567400-50570600	Weak transcription	Fetal Thymus	thymus
15	chr15:50567400-50579600	Weak transcription	Thymus	Thymus
16	chr15:50567600-50579600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:50567600-50579600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:50567600-50593000	Weak transcription	NHDF-Ad	bronchial
19	chr15:50567800-50579800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr15:50568000-50593400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:50568200-50571000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr15:50568200-50572400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr15:50568200-50576200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr15:50568200-50579600	Weak transcription	Osteobl	bone
25	chr15:50568200-50592000	Weak transcription	NHLF	lung
26	chr15:50568400-50571800	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr15:50568400-50576000	Weak transcription	Liver	Liver
28	chr15:50568400-50576000	Weak transcription	HSMM	muscle
29	chr15:50568400-50577600	Weak transcription	NH-A	brain
30	chr15:50568600-50579600	Weak transcription	Fetal Intestine Large	intestine
31	chr15:50568600-50580000	Weak transcription	Esophagus	oesophagus
32	chr15:50568800-50570600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:50568800-50572400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:50568800-50576000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:50568800-50582000	Weak transcription	Stomach Mucosa	stomach
36	chr15:50568800-50591800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr15:50568800-50592200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr15:50568800-50599200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr15:50569000-50576200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr15:50569000-50576200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr15:50569000-50578600	Weak transcription	Fetal Muscle Leg	muscle
42	chr15:50569000-50579600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:50569200-50576000	Weak transcription	A549	lung
44	chr15:50569200-50579600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr15:50569200-50579600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr15:50569200-50591800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:50569200-50592200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr15:50569400-50571000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr15:50569400-50576000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr15:50569600-50571000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links