Variant report

Variant	rs2695163
Chromosome Location	chr15:42041712-42041713
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	chr15:42035386..42037537-chr15:42041123..42043627,2	MCF-7	breast:
2	chr15:42040960..42042477-chr15:42049684..42052512,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174197	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1008710	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs10152332	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10152364	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10775122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs10775123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10775124	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1081022	1.00[CEU][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11070345	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070350	0.81[EUR][1000 genomes]
rs11632100	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11634840	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855017	0.87[ASN][1000 genomes]
rs1197666	1.00[CEU][hapmap]
rs1197670	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1197704	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap]
rs1197768	0.97[ASN][1000 genomes]
rs1197769	0.97[ASN][1000 genomes]
rs1197772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12148330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12441249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12915325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12916992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1648827	0.81[EUR][1000 genomes]
rs1648828	0.81[EUR][1000 genomes]
rs1648829	0.80[EUR][1000 genomes]
rs1648830	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs1648831	0.81[EUR][1000 genomes]
rs1648832	0.81[EUR][1000 genomes]
rs1648833	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs1648834	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1648835	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes]
rs1672464	0.81[EUR][1000 genomes]
rs1672465	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1672466	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs16972089	0.93[CEU][hapmap]
rs16972136	1.00[CEU][hapmap];0.91[MEX][hapmap]
rs1867416	0.90[ASN][1000 genomes]
rs1867417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880937	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880938	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1899819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1899820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1899821	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1918314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2009310	0.85[ASN][1000 genomes]
rs2141141	0.93[ASN][1000 genomes]
rs2178004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2250964	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577952	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577953	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577955	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577958	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2577959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2605569	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2605570	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs2695162	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695166	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2695168	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695169	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695170	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2918051	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2925337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2950446	0.89[ASN][1000 genomes]
rs4244585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.81[ASN][1000 genomes]
rs4270151	0.86[ASN][1000 genomes]
rs4371125	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4465584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4923908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924568	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924571	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57498313	0.81[EUR][1000 genomes]
rs62002069	0.93[ASN][1000 genomes]
rs6493008	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493010	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7164209	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7165230	0.81[EUR][1000 genomes]
rs7169496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169668	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7176474	0.83[ASN][1000 genomes]
rs7177911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8027390	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8028886	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8030179	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8034261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8038148	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8038783	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8039440	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs890508	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv1038894	chr15:42038152-42077452	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2695163	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 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	chr15:42003800-42056000	Weak transcription	Colonic Mucosa	Colon
3	chr15:42009800-42056800	Weak transcription	Fetal Heart	heart
4	chr15:42017400-42062600	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr15:42019400-42060600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr15:42025000-42045800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:42025200-42065400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:42025800-42045000	Weak transcription	Stomach Mucosa	stomach
9	chr15:42029000-42052200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:42029000-42054200	Weak transcription	Small Intestine	intestine
11	chr15:42029200-42048400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:42030400-42046400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:42035400-42054400	Weak transcription	Pancreas	Pancrea
14	chr15:42035600-42046600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr15:42035800-42047600	Weak transcription	NHEK	skin
16	chr15:42035800-42058200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:42036000-42052800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:42036000-42058400	Weak transcription	Psoas Muscle	Psoas
19	chr15:42037000-42044200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:42038800-42051000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr15:42039000-42044800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:42039000-42064400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:42039400-42043600	Strong transcription	Hela-S3	cervix
24	chr15:42039600-42042400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:42039600-42042600	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr15:42039600-42042800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:42039600-42042800	Strong transcription	Fetal Muscle Leg	muscle
28	chr15:42039600-42042800	Strong transcription	GM12878-XiMat	blood
29	chr15:42039600-42043000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:42039600-42043000	Strong transcription	Fetal Brain Female	brain
31	chr15:42039600-42044000	Strong transcription	Fetal Intestine Large	intestine
32	chr15:42039600-42044200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr15:42039600-42049000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:42039600-42062600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr15:42039800-42042200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:42039800-42042800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr15:42039800-42043000	Strong transcription	Primary B cells from cord blood	blood
38	chr15:42039800-42043200	Strong transcription	Fetal Thymus	thymus
39	chr15:42039800-42043400	Strong transcription	Primary hematopoietic stem cells	blood
40	chr15:42039800-42044200	Strong transcription	Primary T cells from cord blood	blood
41	chr15:42039800-42044200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr15:42039800-42044600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:42039800-42049200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:42040000-42042600	Strong transcription	Thymus	Thymus
45	chr15:42040000-42043200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:42040000-42043200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr15:42040000-42049600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:42040000-42061400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr15:42040200-42042000	Strong transcription	Right Ventricle	heart
50	chr15:42040200-42042000	Strong transcription	Stomach Smooth Muscle	stomach

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