Variant report

Variant	rs2605569
Chromosome Location	chr15:42074016-42074017
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42073003..42074739-chr15:42093274..42095961,2	MCF-7	breast:
2	chr15:42064976..42070217-chr15:42070811..42075517,5	K562	blood:
3	chr15:42066709..42068475-chr15:42073432..42076353,2	K562	blood:

Variant related genes	Relation type
ENSG00000137802	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10152332	0.90[EUR][1000 genomes]
rs10152364	0.90[EUR][1000 genomes]
rs10775123	0.88[EUR][1000 genomes]
rs10775124	0.88[EUR][1000 genomes]
rs1081022	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070345	0.88[EUR][1000 genomes]
rs11070347	0.90[EUR][1000 genomes]
rs11632100	0.88[EUR][1000 genomes]
rs11855017	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11857301	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1197704	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1197768	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1197769	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1197772	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12148330	0.90[EUR][1000 genomes]
rs12915325	0.90[EUR][1000 genomes]
rs12916992	0.89[EUR][1000 genomes]
rs16972089	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16972136	0.88[EUR][1000 genomes]
rs1867416	0.84[EUR][1000 genomes]
rs1867417	0.88[EUR][1000 genomes]
rs1880937	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1880938	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1899820	0.88[EUR][1000 genomes]
rs1899821	0.88[EUR][1000 genomes]
rs1918314	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2141141	0.87[EUR][1000 genomes]
rs2178004	0.90[EUR][1000 genomes]
rs2250964	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577947	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577950	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577951	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577952	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577953	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577954	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577955	0.81[ASN][1000 genomes]
rs2577958	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2577959	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2605570	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2695162	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2695163	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2695164	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2695165	0.88[ASN][1000 genomes]
rs2695166	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2695168	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2695169	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2695170	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2918051	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2925337	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2950446	0.82[EUR][1000 genomes]
rs4244585	0.86[EUR][1000 genomes]
rs4923908	0.89[EUR][1000 genomes]
rs4924568	0.88[EUR][1000 genomes]
rs4924571	0.88[EUR][1000 genomes]
rs4924572	0.89[EUR][1000 genomes]
rs62002069	0.84[EUR][1000 genomes]
rs6493008	0.90[EUR][1000 genomes]
rs6493010	0.87[EUR][1000 genomes]
rs7169496	0.89[EUR][1000 genomes]
rs7169668	0.88[EUR][1000 genomes]
rs7177911	0.88[EUR][1000 genomes]
rs7178205	0.88[EUR][1000 genomes]
rs8027390	0.90[EUR][1000 genomes]
rs8034261	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
rs2605569	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42067600-42083000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr15:42068000-42075200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:42068000-42078800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:42068200-42082600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:42068400-42074600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:42068400-42075200	Weak transcription	Pancreas	Pancrea
7	chr15:42068400-42081800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:42068600-42081600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:42068800-42074400	Weak transcription	Primary B cells from cord blood	blood
10	chr15:42068800-42074400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr15:42069200-42075200	Weak transcription	K562	blood
12	chr15:42069400-42075200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:42069800-42075200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:42069800-42075200	Weak transcription	Gastric	stomach
15	chr15:42069800-42081800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:42070000-42081600	Weak transcription	Aorta	Aorta
17	chr15:42070000-42082600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr15:42070200-42109800	Weak transcription	Fetal Brain Male	brain
19	chr15:42070800-42075000	Weak transcription	Dnd41	blood
20	chr15:42071000-42074800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:42071000-42082400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:42071000-42082800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:42071000-42092800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:42071200-42074400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:42071200-42074600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:42071200-42092000	Weak transcription	Brain Germinal Matrix	brain
27	chr15:42072200-42074800	Weak transcription	Esophagus	oesophagus
28	chr15:42072400-42074400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr15:42072400-42074600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:42072400-42075600	Weak transcription	Lung	lung
31	chr15:42072400-42077400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:42072400-42080400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr15:42072400-42080800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:42072400-42081600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:42072600-42075200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:42072600-42075200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:42072600-42075200	Weak transcription	HSMM	muscle
38	chr15:42072600-42080600	Weak transcription	Primary T cells from cord blood	blood
39	chr15:42072600-42081200	Weak transcription	HSMMtube	muscle
40	chr15:42072600-42081800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr15:42072600-42081800	Weak transcription	NH-A	brain
42	chr15:42072600-42082600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr15:42072800-42074600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr15:42072800-42074600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:42072800-42074600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr15:42072800-42074800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr15:42072800-42074800	Weak transcription	Ovary	ovary
48	chr15:42072800-42075200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr15:42072800-42075200	Weak transcription	Spleen	Spleen
50	chr15:42072800-42080600	Weak transcription	Brain Anterior Caudate	brain

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