Variant report

Variant	rs11070686
Chromosome Location	chr15:49615325-49615326
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:49611218..49613140-chr15:49613508..49615931,2	K562	blood:

Variant related genes	Relation type
ENSG00000156958	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11636671	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12440534	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1904317	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2243899	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2246995	0.80[AFR][1000 genomes]
rs2413936	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2413939	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2413942	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2580924	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2940747	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3098614	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3105865	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3105867	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4775803	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs485182	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs520949	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs532209	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs568994	0.80[AFR][1000 genomes]
rs586758	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs641077	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6493364	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8032650	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8041781	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8041823	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9920772	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11070686	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49558000-49624400	Weak transcription	Esophagus	oesophagus
2	chr15:49562200-49626000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:49566600-49623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:49573800-49622200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:49580600-49615600	Weak transcription	Fetal Brain Male	brain
6	chr15:49582600-49628200	Weak transcription	Spleen	Spleen
7	chr15:49586000-49617000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:49594000-49619400	Weak transcription	Stomach Mucosa	stomach
9	chr15:49596800-49620200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:49597200-49622200	Weak transcription	NH-A	brain
11	chr15:49597200-49624800	Weak transcription	Fetal Kidney	kidney
12	chr15:49597400-49624200	Weak transcription	K562	blood
13	chr15:49599200-49636800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:49602400-49615400	Weak transcription	Fetal Heart	heart
15	chr15:49606400-49622200	Weak transcription	HSMM	muscle
16	chr15:49607000-49622200	Weak transcription	NHDF-Ad	bronchial
17	chr15:49607200-49623800	Weak transcription	Psoas Muscle	Psoas
18	chr15:49607600-49624400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:49607800-49622200	Weak transcription	Brain Substantia Nigra	brain
20	chr15:49608000-49615800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr15:49608000-49631800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:49608200-49615400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:49608400-49615600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:49608600-49615600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr15:49608600-49615600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr15:49608600-49631800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr15:49609200-49615800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr15:49609600-49621200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr15:49610400-49622400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:49611000-49615800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr15:49611000-49615800	Strong transcription	Liver	Liver
32	chr15:49611000-49616000	Strong transcription	Primary T cells from cord blood	blood
33	chr15:49611000-49616200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr15:49611000-49616400	Strong transcription	Primary hematopoietic stem cells	blood
35	chr15:49611400-49615600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:49611800-49616000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:49612000-49624200	Weak transcription	Lung	lung
38	chr15:49612200-49623200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr15:49612200-49631600	Weak transcription	Fetal Intestine Small	intestine
40	chr15:49612200-49639000	Weak transcription	NHEK	skin
41	chr15:49612600-49620800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:49612600-49622200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:49612600-49639400	Weak transcription	Right Ventricle	heart
44	chr15:49612800-49615800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr15:49612800-49620200	Weak transcription	Dnd41	blood
46	chr15:49612800-49626600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:49612800-49638000	Weak transcription	Brain Angular Gyrus	brain
48	chr15:49613000-49615400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:49613000-49615400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr15:49613000-49616000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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