Variant report

Variant	rs586758
Chromosome Location	chr15:49508572-49508573
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49508403..49508991-chr15:49517505..49518356,2	MCF-7	breast:
2	chr15:49464598..49467246-chr15:49506406..49508580,2	K562	blood:
3	chr15:49462386..49464017-chr15:49507382..49510117,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156958	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11070681	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs11070686	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11636671	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11636795	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs11852524	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[MEX][hapmap]
rs11858114	0.83[ASW][hapmap];0.95[GIH][hapmap]
rs12101599	0.86[CHB][hapmap];0.86[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12898709	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12900001	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs12913745	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs12917024	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs16962243	0.83[JPT][hapmap]
rs1904317	1.00[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];0.88[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2086256	0.83[ASW][hapmap];0.92[GIH][hapmap]
rs2127242	0.83[ASW][hapmap];0.92[GIH][hapmap]
rs2219812	0.83[ASW][hapmap];0.92[GIH][hapmap]
rs2243899	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2246995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2413936	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413939	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2580924	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940747	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3098614	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]
rs3098620	0.83[ASW][hapmap];0.95[GIH][hapmap]
rs3105861	0.90[YRI][hapmap]
rs3105865	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[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];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3105867	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4775803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs520949	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532209	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs568994	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs641077	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493363	0.83[ASW][hapmap];0.92[GIH][hapmap]
rs6493364	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6493369	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap]
rs8025952	0.81[YRI][hapmap]
rs8032650	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8041781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8041823	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9920772	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039220	chr15:49492509-49644261	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs586758	GALK2	Cis_1M	lymphoblastoid	RTeQTL
rs586758	DTWD1	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49463600-49517600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:49463600-49527800	Weak transcription	HSMM	muscle
3	chr15:49463600-49540200	Weak transcription	Colonic Mucosa	Colon
4	chr15:49480000-49510600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:49484200-49519400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:49487000-49510600	Weak transcription	Thymus	Thymus
7	chr15:49487200-49531200	Weak transcription	HMEC	breast
8	chr15:49491400-49510600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:49492000-49517600	Weak transcription	NHLF	lung
10	chr15:49492000-49520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:49492000-49527800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:49492000-49530200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr15:49492000-49539400	Weak transcription	Small Intestine	intestine
14	chr15:49492200-49512800	Weak transcription	NHDF-Ad	bronchial
15	chr15:49492800-49514600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:49493000-49520000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr15:49494000-49518600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr15:49495000-49509400	Weak transcription	K562	blood
19	chr15:49495000-49510600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:49495000-49515600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:49495000-49515800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr15:49495000-49518000	Weak transcription	Placenta	Placenta
23	chr15:49495200-49520200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:49495400-49510400	Weak transcription	Osteobl	bone
25	chr15:49496000-49512400	Weak transcription	HUVEC	blood vessel
26	chr15:49496200-49510600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr15:49499200-49509000	Weak transcription	Dnd41	blood
28	chr15:49502200-49510800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:49503200-49511000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:49503400-49510600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr15:49503400-49511000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr15:49503600-49524000	Weak transcription	HepG2	liver
33	chr15:49503800-49510800	Weak transcription	Liver	Liver
34	chr15:49504000-49509200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr15:49504000-49510600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:49504000-49511000	Weak transcription	Aorta	Aorta
37	chr15:49504000-49512400	Weak transcription	Fetal Brain Female	brain
38	chr15:49504200-49509400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:49504200-49509400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr15:49504200-49509600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:49504200-49513000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:49504200-49513800	Weak transcription	Fetal Lung	lung
43	chr15:49504200-49520200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr15:49504200-49530800	Weak transcription	Fetal Thymus	thymus
45	chr15:49504600-49508800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr15:49505800-49510600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:49505800-49510600	Weak transcription	Adipose Nuclei	Adipose
48	chr15:49506000-49508600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:49506000-49510600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:49506400-49513600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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