Variant report

Variant	rs3098614
Chromosome Location	chr15:49470870-49470871
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49445500..49448180-chr15:49469776..49471285,2	K562	blood:
2	chr15:49445500..49449019-chr15:49469042..49472548,3	K562	blood:
3	chr15:49462491..49464314-chr15:49469234..49471225,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COPS2-3	chr15:49470576-49470938	NONHSAT042375

Variant related genes	Relation type
ENSG00000166200	Chromatin interaction
ENSG00000259467	Chromatin interaction
ENSG00000156958	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11070681	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs11070686	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11636671	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11858114	0.92[GIH][hapmap]
rs12101599	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.84[YRI][hapmap]
rs12440534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12898709	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12917024	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs16962243	0.82[JPT][hapmap]
rs1904317	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2086256	0.90[GIH][hapmap]
rs2127242	0.90[GIH][hapmap]
rs2219812	0.90[GIH][hapmap]
rs2243899	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2246995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2413936	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413939	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2413942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2580924	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2940747	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3098620	0.92[GIH][hapmap]
rs3105861	0.90[YRI][hapmap]
rs3105865	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3105867	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4468544	0.82[ASN][1000 genomes]
rs4775803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs485182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs520949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs532209	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568994	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs586758	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs641077	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493363	0.90[GIH][hapmap]
rs6493364	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7497114	0.82[ASN][1000 genomes]
rs8025952	0.81[YRI][hapmap]
rs8032650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8041781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8041823	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3098614	GALK2	Cis_1M	lymphoblastoid	RTeQTL
rs3098614	DTWD1	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49463000-49479600	Weak transcription	Left Ventricle	heart
2	chr15:49463200-49471800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr15:49463200-49472000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:49463200-49472000	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:49463200-49479600	Weak transcription	Right Ventricle	heart
6	chr15:49463200-49479800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr15:49463200-49508200	Weak transcription	Ovary	ovary
8	chr15:49463400-49480000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr15:49463600-49471400	Weak transcription	Fetal Muscle Leg	muscle
10	chr15:49463600-49472400	Weak transcription	HUVEC	blood vessel
11	chr15:49463600-49474200	Weak transcription	Fetal Stomach	stomach
12	chr15:49463600-49474400	Weak transcription	Primary B cells from cord blood	blood
13	chr15:49463600-49477200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:49463600-49479400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:49463600-49479600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr15:49463600-49494400	Weak transcription	Fetal Thymus	thymus
17	chr15:49463600-49517600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:49463600-49527800	Weak transcription	HSMM	muscle
19	chr15:49463600-49540200	Weak transcription	Colonic Mucosa	Colon
20	chr15:49463800-49471600	Weak transcription	HMEC	breast
21	chr15:49463800-49472400	Weak transcription	Fetal Brain Female	brain
22	chr15:49463800-49472600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr15:49463800-49472600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr15:49463800-49472800	Weak transcription	Fetal Lung	lung
25	chr15:49463800-49479200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:49463800-49479400	Weak transcription	Osteobl	bone
27	chr15:49464000-49474400	Weak transcription	NHDF-Ad	bronchial
28	chr15:49464000-49482800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr15:49464000-49491600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:49464200-49471600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr15:49464200-49471600	Weak transcription	NHEK	skin
32	chr15:49464200-49477400	Weak transcription	Fetal Intestine Large	intestine
33	chr15:49464200-49479200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:49464200-49479400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:49464200-49481800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:49464400-49493800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr15:49464400-49493800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr15:49464400-49500000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:49464800-49477400	Weak transcription	Primary T cells from cord blood	blood
40	chr15:49464800-49479600	Weak transcription	NHLF	lung
41	chr15:49464800-49481800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr15:49465200-49472200	Weak transcription	Dnd41	blood
43	chr15:49465200-49494000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr15:49465400-49477400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr15:49465400-49479600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:49465400-49508200	Weak transcription	Hela-S3	cervix
47	chr15:49465600-49471600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:49465600-49471800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr15:49466800-49482800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr15:49467400-49471600	Weak transcription	Small Intestine	intestine

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