Variant report

Variant	rs11858114
Chromosome Location	chr15:49538159-49538160
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	chr15:49535482..49538280-chr15:49538929..49540490,2	K562	blood:
2	chr15:49470039..49472415-chr15:49535845..49538837,2	K562	blood:

Variant related genes	Relation type
ENSG00000259545	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10467992	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1048975	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10775139	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10851475	0.88[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs11070682	1.00[CHB][hapmap]
rs11070692	0.92[CEU][hapmap];0.81[CHB][hapmap]
rs11629547	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11632063	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633810	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs12101599	0.84[ASW][hapmap]
rs12438777	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs12902875	0.81[ASN][1000 genomes]
rs12904344	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs1429556	0.92[CEU][hapmap];0.80[CHB][hapmap]
rs1812926	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1864299	0.85[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap]
rs1904317	0.82[ASW][hapmap];0.92[GIH][hapmap]
rs1981995	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2086256	1.00[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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2127241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2127242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2127244	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2169932	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2219812	1.00[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];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2247517	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2263559	0.98[ASN][1000 genomes]
rs2413935	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2413937	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2413939	0.82[AMR][1000 genomes]
rs2413942	0.84[YRI][hapmap]
rs2457228	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2580923	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2580926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2663088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2663089	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2663090	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28437582	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28479967	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28539950	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28728368	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28731311	0.96[ASN][1000 genomes]
rs2899427	1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs2899430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899431	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs2919148	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940745	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2940746	0.98[ASN][1000 genomes]
rs3098613	0.85[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs3098614	0.92[GIH][hapmap]
rs3098615	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3098619	0.85[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs3098620	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3098621	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3105858	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3105861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3105863	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3105864	0.85[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs3105865	0.83[ASW][hapmap];0.95[GIH][hapmap]
rs3105866	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs34854443	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3907313	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4316697	0.92[CEU][hapmap];0.81[CHB][hapmap];0.92[MEX][hapmap]
rs4774537	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4775804	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775805	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4775807	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs481466	0.85[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs489813	0.89[CHB][hapmap]
rs490621	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs500122	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520949	0.92[GIH][hapmap]
rs55736202	0.96[ASN][1000 genomes]
rs563533	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs568726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs586758	0.83[ASW][hapmap];0.95[GIH][hapmap]
rs600863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603868	0.92[ASN][1000 genomes]
rs604765	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs612803	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs626295	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs626855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs641077	0.83[ASW][hapmap];0.95[GIH][hapmap]
rs647118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs6493356	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs6493357	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs6493361	0.96[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6493363	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs671945	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs679957	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]
rs685172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7166847	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7167338	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7167555	0.85[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176455	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7179127	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs735495	0.88[CEU][hapmap]
rs754165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs754166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8025952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8032650	0.92[GIH][hapmap]
rs8034661	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8034747	0.92[CEU][hapmap]
rs8039512	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs8040075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9806748	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11858114	SPATA5L1	cis	parietal	SCAN
rs11858114	DTWD1	cis	cerebellum	SCAN
rs11858114	GALK2	cis	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49463600-49540200	Weak transcription	Colonic Mucosa	Colon
2	chr15:49492000-49539400	Weak transcription	Small Intestine	intestine
3	chr15:49510000-49541800	Weak transcription	NHEK	skin
4	chr15:49518000-49541000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:49518200-49548600	Weak transcription	Aorta	Aorta
6	chr15:49518600-49557600	Weak transcription	Esophagus	oesophagus
7	chr15:49518800-49539200	Weak transcription	Ovary	ovary
8	chr15:49520400-49595600	Weak transcription	Right Ventricle	heart
9	chr15:49522000-49538200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr15:49522000-49540400	Weak transcription	Stomach Mucosa	stomach
11	chr15:49522400-49559400	Weak transcription	Pancreas	Pancrea
12	chr15:49523800-49540200	Weak transcription	Spleen	Spleen
13	chr15:49524600-49539200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:49524600-49544800	Weak transcription	Lung	lung
15	chr15:49528000-49539600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:49528000-49576000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:49528400-49547800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr15:49529200-49550600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:49529400-49539800	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:49529400-49540200	Weak transcription	Fetal Brain Female	brain
21	chr15:49529400-49544200	Weak transcription	Brain Anterior Caudate	brain
22	chr15:49529400-49545600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr15:49529600-49541600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr15:49530000-49539200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:49530800-49538600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr15:49531000-49540400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr15:49531000-49540600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:49531000-49542800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr15:49531200-49538800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr15:49531200-49540000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr15:49531600-49539400	Weak transcription	Psoas Muscle	Psoas
32	chr15:49531800-49539400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:49532000-49545000	Weak transcription	Fetal Thymus	thymus
34	chr15:49532200-49539200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr15:49532200-49539400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:49532200-49542600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:49532800-49545400	Weak transcription	HUVEC	blood vessel
38	chr15:49533000-49541400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr15:49533400-49548200	Weak transcription	HMEC	breast
40	chr15:49533600-49538800	Weak transcription	Adipose Nuclei	Adipose
41	chr15:49533800-49576200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:49534600-49539600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr15:49535200-49539000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:49535200-49540000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:49535400-49539600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:49535600-49539000	Weak transcription	Colon Smooth Muscle	Colon
47	chr15:49535600-49541200	Weak transcription	Fetal Kidney	kidney
48	chr15:49535600-49557000	Weak transcription	Fetal Intestine Small	intestine
49	chr15:49535600-49564600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr15:49535600-49574200	Weak transcription	Rectal Mucosa Donor 31	rectum

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