Variant report

Variant	rs12902271
Chromosome Location	chr15:49544897-49544898
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10519224	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10519225	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11853969	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11854039	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11854557	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11855798	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11857515	1.00[YRI][hapmap]
rs11858814	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12591300	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12899422	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12900838	0.81[ASN][1000 genomes]
rs12901353	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12901929	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12902096	0.84[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12905094	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12905477	0.84[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12914876	1.00[YRI][hapmap]
rs12916839	1.00[YRI][hapmap]
rs17393761	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17435932	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17472989	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17478694	1.00[YRI][hapmap]
rs17478785	1.00[YRI][hapmap]
rs1961393	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2289389	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34562714	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs34748066	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs36023246	0.86[AFR][1000 genomes]
rs36100631	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4389093	1.00[YRI][hapmap]
rs4774538	0.86[AFR][1000 genomes]
rs4775806	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4775808	0.82[AFR][1000 genomes]
rs55979115	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62009762	0.81[ASN][1000 genomes]
rs62009834	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs71467664	0.81[ASN][1000 genomes]
rs7180168	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7497335	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8029687	0.91[ASN][1000 genomes]
rs8043493	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 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
17	esv3508350	chr15:49543710-49549008	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv3311210	chr15:49544060-49548858	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
19	esv3508349	chr15:49544110-49548908	Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	esv3508354	chr15:49544404-49548543	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	esv3311209	chr15:49544434-49548137	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	esv3508355	chr15:49544719-49547965	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
23	esv3311206	chr15:49544726-49547931	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
24	esv3311211	chr15:49544727-49547945	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
25	esv3508351	chr15:49544733-49547936	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
26	esv3508348	chr15:49544741-49547897	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
27	esv3508353	chr15:49544769-49547904	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
28	esv17257	chr15:49544776-49547871	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
29	esv3311207	chr15:49544783-49547927	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
30	esv3311205	chr15:49544797-49547880	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
31	esv3311212	chr15:49544864-49547855	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
32	esv3508356	chr15:49544864-49547855	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12902271	COPS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49518200-49548600	Weak transcription	Aorta	Aorta
2	chr15:49518600-49557600	Weak transcription	Esophagus	oesophagus
3	chr15:49520400-49595600	Weak transcription	Right Ventricle	heart
4	chr15:49522400-49559400	Weak transcription	Pancreas	Pancrea
5	chr15:49528000-49576000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:49528400-49547800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr15:49529200-49550600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:49529400-49545600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:49532000-49545000	Weak transcription	Fetal Thymus	thymus
10	chr15:49532800-49545400	Weak transcription	HUVEC	blood vessel
11	chr15:49533400-49548200	Weak transcription	HMEC	breast
12	chr15:49533800-49576200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:49535600-49557000	Weak transcription	Fetal Intestine Small	intestine
14	chr15:49535600-49564600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr15:49535600-49574200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr15:49535600-49574200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr15:49535800-49545000	Weak transcription	Thymus	Thymus
18	chr15:49535800-49545600	Weak transcription	Fetal Intestine Large	intestine
19	chr15:49535800-49549200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:49535800-49563400	Weak transcription	NH-A	brain
21	chr15:49535800-49566800	Weak transcription	Left Ventricle	heart
22	chr15:49535800-49575800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:49536000-49546800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr15:49536200-49547600	Weak transcription	Hela-S3	cervix
25	chr15:49536200-49549400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:49536200-49549800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr15:49536200-49553200	Weak transcription	Primary B cells from cord blood	blood
28	chr15:49537600-49566000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:49537800-49549000	Weak transcription	Liver	Liver
30	chr15:49538600-49550400	Weak transcription	HSMM	muscle
31	chr15:49539400-49553200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:49539600-49563000	Weak transcription	Ovary	ovary
33	chr15:49540000-49550400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr15:49540000-49550400	Weak transcription	NHDF-Ad	bronchial
35	chr15:49540000-49552200	Weak transcription	Fetal Muscle Leg	muscle
36	chr15:49540000-49566200	Weak transcription	K562	blood
37	chr15:49540000-49577600	Weak transcription	Small Intestine	intestine
38	chr15:49540200-49545600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr15:49540200-49552200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:49540600-49557400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr15:49540800-49548400	Weak transcription	Colon Smooth Muscle	Colon
42	chr15:49541200-49547800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:49541400-49551400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:49541400-49562600	Weak transcription	Dnd41	blood
45	chr15:49541600-49545400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr15:49541600-49548400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:49541600-49557200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:49541600-49575000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr15:49541600-49595800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr15:49541800-49545400	Weak transcription	Fetal Lung	lung

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