Variant report

Variant	rs2605570
Chromosome Location	chr15:42059521-42059522
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42057695..42060006-chr15:42069588..42072427,2	K562	blood:
2	chr15:42057536..42062634-chr15:42063486..42067728,8	K562	blood:
3	chr15:42058854..42060510-chr15:42065051..42067133,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260814	Chromatin interaction
ENSG00000137802	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1008710	0.85[CEU][hapmap];0.82[CHB][hapmap]
rs10152332	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10152364	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10775122	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs10775123	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10775124	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1081022	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11070345	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11070347	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11632100	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11634840	0.87[ASN][1000 genomes]
rs11855017	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1197666	0.82[CEU][hapmap]
rs1197670	0.86[ASN][1000 genomes]
rs1197704	0.90[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1197768	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1197769	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1197772	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12148330	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12441249	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs12915325	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12916992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1648830	0.85[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap]
rs1648833	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs1648834	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs1648835	0.83[CEU][hapmap]
rs1672465	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs1672466	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs16972089	0.86[EUR][1000 genomes]
rs16972136	0.83[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs1867416	0.86[ASN][1000 genomes]
rs1867417	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1880937	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1880938	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1899819	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1899820	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1899821	0.85[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1918314	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs2009310	0.80[ASN][1000 genomes]
rs2141141	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2178004	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2250964	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2577947	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2577950	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2577951	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs2577952	0.85[ASN][1000 genomes]
rs2577953	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2577954	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2577955	0.89[ASN][1000 genomes]
rs2577958	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2577959	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs2605569	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2695162	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2695163	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs2695164	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2695166	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2695168	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2695169	0.85[CEU][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2695170	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2918051	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2925337	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2950446	0.84[ASN][1000 genomes]
rs3743028	0.84[ASN][1000 genomes]
rs4244585	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs4270151	0.82[ASN][1000 genomes]
rs4371125	0.90[CHB][hapmap];0.89[ASN][1000 genomes]
rs4465584	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4923908	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924568	0.83[CEU][hapmap];0.90[CHB][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924571	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924572	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62002069	0.89[ASN][1000 genomes]
rs6493008	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6493010	0.82[EUR][1000 genomes]
rs7164209	0.89[ASN][1000 genomes]
rs7169496	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7169668	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7177911	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7178205	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8027390	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8028886	0.86[ASN][1000 genomes]
rs8034261	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8038148	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs8038783	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs8039440	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	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
5	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
6	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
7	esv2757597	chr15:42047173-42122617	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	esv2760027	chr15:42047173-42122617	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv904113	chr15:42050390-42118971	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription 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 target site	19 gene(s)	inside rSNPs	diseases
10	nsv904114	chr15:42050390-42119900	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2605570	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	chr15:42017400-42062600	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr15:42019400-42060600	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr15:42025200-42065400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:42039000-42064400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:42039600-42062600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr15:42040000-42061400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr15:42040200-42059800	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr15:42040200-42064400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:42040600-42063000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr15:42044400-42062600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr15:42045600-42060000	Strong transcription	Primary B cells from cord blood	blood
13	chr15:42045600-42061600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:42045600-42062000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:42045600-42065200	Weak transcription	Stomach Mucosa	stomach
16	chr15:42045800-42063200	Strong transcription	Placenta	Placenta
17	chr15:42046000-42061400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:42046000-42062600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:42046200-42062800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr15:42046400-42060400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr15:42050200-42059600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:42051000-42062400	Strong transcription	Primary T cells from cord blood	blood
23	chr15:42051000-42062400	Strong transcription	Liver	Liver
24	chr15:42051200-42061200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:42051600-42060000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr15:42051600-42061800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:42051600-42062400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr15:42051800-42060200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:42051800-42060400	Strong transcription	Brain Germinal Matrix	brain
30	chr15:42051800-42061200	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:42051800-42061800	Strong transcription	Fetal Intestine Large	intestine
32	chr15:42051800-42062400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:42051800-42062400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:42052000-42061000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr15:42052000-42061200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:42052000-42063000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:42052200-42059800	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr15:42052200-42059800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:42052200-42060000	Strong transcription	Adipose Nuclei	Adipose
40	chr15:42052200-42060000	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr15:42052200-42061400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:42052200-42062000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:42052200-42062400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:42052200-42062400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr15:42052200-42062400	Strong transcription	Fetal Muscle Leg	muscle
46	chr15:42052200-42062800	Strong transcription	Fetal Thymus	thymus
47	chr15:42052400-42059600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:42052400-42059600	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr15:42052400-42060000	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr15:42052400-42060000	Strong transcription	Sigmoid Colon	Sigmoid Colon

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