Variant report

Variant	rs679957
Chromosome Location	chr15:49440532-49440533
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49429242..49431810-chr15:49437695..49440967,3	K562	blood:
2	chr15:49440196..49442233-chr15:49445854..49447948,2	MCF-7	breast:
3	chr15:49439437..49443597-chr15:49460944..49463407,4	MCF-7	breast:
4	chr15:49438116..49443617-chr15:49443933..49448726,7	K562	blood:
5	chr15:49411597..49414274-chr15:49439381..49441889,2	K562	blood:
6	chr15:49336910..49339486-chr15:49439090..49441329,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200120	Chromatin interaction
ENSG00000138593	Chromatin interaction
ENSG00000156958	Chromatin interaction
ENSG00000259467	Chromatin interaction
ENSG00000264210	Chromatin interaction
ENSG00000166200	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1048975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10775139	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10851475	0.88[CEU][hapmap]
rs11070682	1.00[CHB][hapmap]
rs11629547	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11632063	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11633810	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs11858114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12438777	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs12440709	0.84[ASN][1000 genomes]
rs12442679	0.85[ASN][1000 genomes]
rs12898691	0.84[ASN][1000 genomes]
rs12902875	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12904344	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1812926	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1864299	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs1981995	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2086256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2127241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2127242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2127244	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2169932	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2219812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2247517	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2263559	0.92[ASN][1000 genomes]
rs2413931	0.82[ASN][1000 genomes]
rs2413935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2413937	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2457228	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2580923	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2580926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2663088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2663089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2663090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28437582	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28479967	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28539950	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28676698	0.81[ASN][1000 genomes]
rs28728368	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28731311	0.93[ASN][1000 genomes]
rs2899427	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2899430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2899431	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2919148	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2940745	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2940746	0.92[ASN][1000 genomes]
rs3098613	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3098615	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3098619	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3098620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3098621	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs3105858	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs3105861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3105863	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3105864	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3105866	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs34854443	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3907313	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4774537	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4775804	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4775805	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4775807	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs481466	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs489813	0.89[CHB][hapmap]
rs490621	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs491277	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs500122	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55736202	0.93[ASN][1000 genomes]
rs563533	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs568726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs600863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs603868	0.98[ASN][1000 genomes]
rs604765	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs612803	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs626295	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs626855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs647118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6493356	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6493357	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs6493361	0.96[CEU][hapmap];0.81[CHB][hapmap]
rs671945	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs685172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7166847	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs7167338	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7167555	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7176455	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7179127	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs754165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs754166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8025952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8039512	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs8040075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs679957	COPS2	Cis_1M	lymphoblastoid	RTeQTL
rs679957	GALK2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49405600-49441800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:49413600-49447000	Weak transcription	Stomach Mucosa	stomach
3	chr15:49419000-49445800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:49420200-49447000	Weak transcription	Spleen	Spleen
5	chr15:49420400-49447000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:49429200-49447000	Weak transcription	Esophagus	oesophagus
7	chr15:49433800-49446600	Weak transcription	Fetal Intestine Small	intestine
8	chr15:49435200-49445800	Weak transcription	Fetal Heart	heart
9	chr15:49435600-49446600	Weak transcription	Right Ventricle	heart
10	chr15:49435800-49440600	Weak transcription	Brain Anterior Caudate	brain
11	chr15:49435800-49440600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:49435800-49440800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:49435800-49442800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:49435800-49442800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:49435800-49443000	Weak transcription	Colonic Mucosa	Colon
16	chr15:49435800-49443000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:49435800-49445400	Weak transcription	Brain Germinal Matrix	brain
18	chr15:49435800-49445600	Weak transcription	Fetal Brain Male	brain
19	chr15:49435800-49445600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr15:49435800-49446000	Weak transcription	Fetal Kidney	kidney
21	chr15:49435800-49446000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:49435800-49446600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:49435800-49446600	Weak transcription	HSMMtube	muscle
24	chr15:49435800-49446800	Weak transcription	Aorta	Aorta
25	chr15:49435800-49446800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr15:49436000-49440600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:49436000-49444800	Weak transcription	Lung	lung
28	chr15:49436000-49445200	Weak transcription	Thymus	Thymus
29	chr15:49436000-49446000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr15:49436000-49446600	Weak transcription	Fetal Stomach	stomach
31	chr15:49436000-49446600	Weak transcription	Fetal Thymus	thymus
32	chr15:49436000-49446800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr15:49436000-49446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:49436000-49447000	Weak transcription	Gastric	stomach
35	chr15:49436000-49447000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:49436200-49446600	Weak transcription	Fetal Lung	lung
37	chr15:49436200-49446600	Weak transcription	Fetal Muscle Leg	muscle
38	chr15:49436200-49447000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:49436400-49441600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:49436400-49447000	Weak transcription	Left Ventricle	heart
41	chr15:49437000-49441600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:49437000-49444600	Weak transcription	Dnd41	blood
43	chr15:49437000-49446600	Weak transcription	Fetal Brain Female	brain
44	chr15:49437200-49440600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:49437200-49440800	Weak transcription	HepG2	liver
46	chr15:49437200-49445200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:49437200-49445800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:49437200-49445800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:49437200-49445800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:49437200-49446000	Weak transcription	H1 Cell Line	embryonic stem cell

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