Variant report

Variant	rs3105866
Chromosome Location	chr15:49427487-49427488
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr15:49427140-49427552	GM12878	blood:	n/a	n/a
2	RUNX3	chr15:49427211-49427539	GM12878	blood:	n/a	n/a
3	MAFK	chr15:49427226-49428362	IMR90	lung:	n/a	chr15:49427759-49427774
4	EP300	chr15:49427406-49427779	GM12878	blood:	n/a	n/a
5	GATA2	chr15:49427274-49428459	HUVEC	blood vessel:	n/a	chr15:49428228-49428244 chr15:49428233-49428240 chr15:49428226-49428247 chr15:49428233-49428243 chr15:49428230-49428244 chr15:49428233-49428240 chr15:49428233-49428240

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49423792..49428339-chr15:49429632..49433589,5	K562	blood:

Variant related genes	Relation type
COPS2	TF binding region
ENSG00000166200	Chromatin interaction
ENSG00000200120	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10467993	0.81[AMR][1000 genomes]
rs1048975	0.89[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10775139	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs10851475	0.85[CHB][hapmap]
rs11070682	0.85[CHB][hapmap]
rs11070683	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11070685	0.87[YRI][hapmap]
rs11070687	0.84[AMR][1000 genomes]
rs11630937	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11632386	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11633810	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11854667	0.80[AMR][1000 genomes]
rs11858114	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12148348	0.87[ASN][1000 genomes]
rs12437486	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12438777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899761	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12909779	0.83[AMR][1000 genomes]
rs12915792	0.83[YRI][hapmap]
rs16962057	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs16962111	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1816293	0.80[AMR][1000 genomes]
rs1864299	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1981995	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2086256	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2127241	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2127242	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2163095	0.83[AMR][1000 genomes]
rs2163096	0.83[AMR][1000 genomes]
rs2219812	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2244224	0.81[YRI][hapmap]
rs2247003	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2247517	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2263559	0.83[EUR][1000 genomes]
rs2264508	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2289390	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2413935	0.89[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2413941	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439133	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2457228	0.89[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2457229	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2580926	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2663088	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2663089	0.89[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2663091	0.81[YRI][hapmap]
rs28566064	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28653543	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28731311	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2899427	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2899428	0.80[YRI][hapmap]
rs2899430	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2899431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2940746	0.83[EUR][1000 genomes]
rs3098613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3098619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3098620	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3098621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3105858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3105861	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3105864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3907313	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4393519	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4421927	0.83[AMR][1000 genomes]
rs4508377	0.83[AMR][1000 genomes]
rs4774537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4775801	0.83[YRI][hapmap]
rs481466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs489813	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs507054	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs520495	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55736202	0.82[EUR][1000 genomes]
rs568726	0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs577614	0.90[YRI][hapmap]
rs58851861	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs600863	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs603868	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs604765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs609434	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs612803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs619045	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62009779	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs626295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs626855	0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs633333	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs647118	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6493356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493359	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6493362	0.84[AMR][1000 genomes]
rs66499252	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs672777	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs679957	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs685172	0.89[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs694882	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7162602	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7166847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7168201	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes]
rs7169443	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7173761	0.80[AMR][1000 genomes]
rs7176697	0.81[YRI][hapmap]
rs7177959	0.86[YRI][hapmap]
rs7179127	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7179237	0.83[AMR][1000 genomes]
rs7179301	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs754165	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs754166	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs8024102	0.84[AMR][1000 genomes]
rs8025952	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs8031480	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs8034956	0.80[AMR][1000 genomes]
rs8039512	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8039920	0.83[AMR][1000 genomes]
rs8040075	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs8040116	0.87[YRI][hapmap]
rs8040134	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs8041461	0.84[AMR][1000 genomes]
rs8182081	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs919447	0.96[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs9806208	0.83[AMR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3105866	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49388800-49434800	Weak transcription	Small Intestine	intestine
2	chr15:49398600-49427600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:49403000-49434600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:49403400-49440200	Weak transcription	Pancreas	Pancrea
5	chr15:49403600-49432200	Weak transcription	Fetal Stomach	stomach
6	chr15:49403600-49435200	Weak transcription	Aorta	Aorta
7	chr15:49403600-49435200	Weak transcription	Gastric	stomach
8	chr15:49403600-49435400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:49403800-49433200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:49404800-49434600	Weak transcription	Right Ventricle	heart
11	chr15:49404800-49435000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:49405600-49441800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:49411400-49432200	Weak transcription	Fetal Intestine Small	intestine
14	chr15:49413600-49447000	Weak transcription	Stomach Mucosa	stomach
15	chr15:49415200-49433400	Weak transcription	Lung	lung
16	chr15:49415400-49427600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:49415600-49437600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr15:49415800-49437400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:49416200-49427600	Weak transcription	Fetal Brain Male	brain
20	chr15:49416200-49437400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr15:49416400-49427800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:49416800-49436800	Strong transcription	Liver	Liver
23	chr15:49416800-49437200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:49417000-49437200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:49417200-49436600	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr15:49417200-49437200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:49417200-49437200	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:49417200-49437400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:49417200-49437400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:49417400-49427600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:49417400-49427600	Strong transcription	Placenta	Placenta
32	chr15:49417400-49437200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr15:49417600-49437200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:49417600-49437200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr15:49417800-49437200	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:49418000-49435800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr15:49418600-49436000	Strong transcription	Fetal Thymus	thymus
38	chr15:49418600-49437600	Strong transcription	Primary B cells from peripheral blood	blood
39	chr15:49418800-49430800	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr15:49418800-49436000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:49418800-49436000	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr15:49418800-49436800	Strong transcription	Adipose Nuclei	Adipose
43	chr15:49418800-49437000	Strong transcription	Dnd41	blood
44	chr15:49419000-49427600	Strong transcription	NHDF-Ad	bronchial
45	chr15:49419000-49431600	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr15:49419000-49437000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:49419000-49445800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr15:49419200-49437000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr15:49419400-49435800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr15:49419400-49436400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links