Variant report

Variant	rs4775803
Chromosome Location	chr15:49541278-49541279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11070681	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11070686	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11631040	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs11636671	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11636795	0.91[CEU][hapmap];0.91[CHB][hapmap]
rs11852524	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs12101599	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12440534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12898709	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12900001	1.00[CHB][hapmap]
rs12913745	0.81[CEU][hapmap]
rs12917024	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs16962243	0.83[JPT][hapmap]
rs1904317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2243899	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2246995	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2413936	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413939	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2413942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2580924	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940747	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3098614	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]
rs3105861	0.81[YRI][hapmap]
rs3105865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3105867	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs485182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs520949	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532209	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs568994	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs586758	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]
rs641077	1.00[CEU][hapmap];0.95[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]
rs6493364	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6493369	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs8032650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8041781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8041823	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9920772	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv569340	chr15:49529302-49547735	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv569341	chr15:49529302-49547790	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv569342	chr15:49529302-49549943	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv569343	chr15:49531192-49547790	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv569344	chr15:49534702-49546105	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv569345	chr15:49534702-49546939	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv569346	chr15:49534702-49547790	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv569347	chr15:49534702-49549943	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv569348	chr15:49540216-49546424	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv569349	chr15:49540216-49546574	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv569350	chr15:49540216-49546683	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv569351	chr15:49540216-49547146	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv569352	chr15:49540216-49547735	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv569353	chr15:49540216-49547790	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv569354	chr15:49540216-49549943	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4775803	GALK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49510000-49541800	Weak transcription	NHEK	skin
2	chr15:49518200-49548600	Weak transcription	Aorta	Aorta
3	chr15:49518600-49557600	Weak transcription	Esophagus	oesophagus
4	chr15:49520400-49595600	Weak transcription	Right Ventricle	heart
5	chr15:49522400-49559400	Weak transcription	Pancreas	Pancrea
6	chr15:49524600-49544800	Weak transcription	Lung	lung
7	chr15:49528000-49576000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:49528400-49547800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:49529200-49550600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:49529400-49544200	Weak transcription	Brain Anterior Caudate	brain
11	chr15:49529400-49545600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr15:49529600-49541600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:49531000-49542800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr15:49532000-49545000	Weak transcription	Fetal Thymus	thymus
15	chr15:49532200-49542600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr15:49532800-49545400	Weak transcription	HUVEC	blood vessel
17	chr15:49533000-49541400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr15:49533400-49548200	Weak transcription	HMEC	breast
19	chr15:49533800-49576200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:49535600-49557000	Weak transcription	Fetal Intestine Small	intestine
21	chr15:49535600-49564600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr15:49535600-49574200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr15:49535600-49574200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:49535800-49541400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr15:49535800-49542000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:49535800-49545000	Weak transcription	Thymus	Thymus
27	chr15:49535800-49545600	Weak transcription	Fetal Intestine Large	intestine
28	chr15:49535800-49549200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:49535800-49563400	Weak transcription	NH-A	brain
30	chr15:49535800-49566800	Weak transcription	Left Ventricle	heart
31	chr15:49535800-49575800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:49536000-49546800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:49536200-49541600	Weak transcription	GM12878-XiMat	blood
34	chr15:49536200-49547600	Weak transcription	Hela-S3	cervix
35	chr15:49536200-49549400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:49536200-49549800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr15:49536200-49553200	Weak transcription	Primary B cells from cord blood	blood
38	chr15:49537200-49541600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:49537600-49566000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:49537800-49549000	Weak transcription	Liver	Liver
41	chr15:49538200-49541800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr15:49538600-49550400	Weak transcription	HSMM	muscle
43	chr15:49539400-49553200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:49539600-49541600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr15:49539600-49543800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:49539600-49544400	Weak transcription	Placenta	Placenta
47	chr15:49539600-49563000	Weak transcription	Ovary	ovary
48	chr15:49539800-49541800	Enhancers	Fetal Lung	lung
49	chr15:49540000-49550400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr15:49540000-49550400	Weak transcription	NHDF-Ad	bronchial

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