Variant report

Variant	rs2695168
Chromosome Location	chr15:42034002-42034003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42030668..42033706-chr15:42033784..42035660,3	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10152332	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10152364	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10775123	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10775124	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070345	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070347	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11632100	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634840	0.90[ASN][1000 genomes]
rs11855017	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1197768	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1197769	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1197772	0.95[ASN][1000 genomes]
rs12148330	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12441249	0.92[ASN][1000 genomes]
rs12915325	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12916992	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16972089	0.82[EUR][1000 genomes]
rs16972136	0.81[EUR][1000 genomes]
rs1867416	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1867417	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1880937	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1880938	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1899820	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1899821	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1918314	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2009310	0.83[ASN][1000 genomes]
rs2141141	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2178004	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2250964	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2577947	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2577950	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2577951	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2577953	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2577954	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2577955	0.92[ASN][1000 genomes]
rs2577958	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2577959	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2605569	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2605570	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2695162	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695163	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695164	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695166	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2695169	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695170	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2918051	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2925337	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2950446	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4244585	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4270151	0.85[ASN][1000 genomes]
rs4371125	0.92[ASN][1000 genomes]
rs4465584	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4923908	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924568	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924571	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924572	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62002069	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493008	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6493010	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7164209	0.92[ASN][1000 genomes]
rs7169496	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7169668	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176474	0.81[ASN][1000 genomes]
rs7177911	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7178205	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8027390	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8028886	0.89[ASN][1000 genomes]
rs8030179	0.81[ASN][1000 genomes]
rs8034261	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8038148	0.89[ASN][1000 genomes]
rs8038783	0.92[ASN][1000 genomes]
rs8039440	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1048655	chr15:41978391-42049360	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
4	nsv1036086	chr15:42004962-42091451	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1041861	chr15:42016097-42062287	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv1054671	chr15:42016097-42098896	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1044347	chr15:42023805-42049360	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2695168	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41972400-42065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:41984200-42034800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:41989000-42041600	Weak transcription	Fetal Brain Male	brain
4	chr15:41996200-42034800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:42003800-42056000	Weak transcription	Colonic Mucosa	Colon
6	chr15:42006200-42034800	Weak transcription	A549	lung
7	chr15:42006400-42041400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:42009800-42056800	Weak transcription	Fetal Heart	heart
9	chr15:42017400-42062600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr15:42019000-42037000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:42019200-42037200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:42019400-42036800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:42019400-42037000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:42019400-42060600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:42020000-42036200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:42020400-42036200	Strong transcription	Fetal Thymus	thymus
17	chr15:42020600-42037000	Strong transcription	Hela-S3	cervix
18	chr15:42021000-42036800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr15:42022400-42036800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr15:42022600-42034800	Weak transcription	Esophagus	oesophagus
21	chr15:42023200-42035000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:42023800-42037000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:42023800-42037200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:42024000-42036800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr15:42024000-42037000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr15:42024000-42037200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr15:42024600-42037000	Strong transcription	Placenta	Placenta
28	chr15:42025000-42034800	Weak transcription	NHLF	lung
29	chr15:42025000-42045800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:42025200-42036000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:42025200-42065400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr15:42025400-42037200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:42025600-42037000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:42025800-42045000	Weak transcription	Stomach Mucosa	stomach
35	chr15:42026400-42035600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr15:42027000-42037800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:42028800-42034600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:42028800-42041200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr15:42029000-42034200	Weak transcription	Pancreas	Pancrea
40	chr15:42029000-42034600	Weak transcription	Brain Cingulate Gyrus	brain
41	chr15:42029000-42034600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:42029000-42034600	Weak transcription	Right Ventricle	heart
43	chr15:42029000-42034800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr15:42029000-42034800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:42029000-42034800	Weak transcription	Gastric	stomach
46	chr15:42029000-42034800	Weak transcription	Spleen	Spleen
47	chr15:42029000-42041400	Weak transcription	Aorta	Aorta
48	chr15:42029000-42052200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr15:42029000-42054200	Weak transcription	Small Intestine	intestine
50	chr15:42029200-42034400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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