Variant report

Variant	rs2577952
Chromosome Location	chr15:42073402-42073403
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	chr15:42073003..42074739-chr15:42093274..42095961,2	MCF-7	breast:
2	chr15:42064976..42070217-chr15:42070811..42075517,5	K562	blood:

Variant related genes	Relation type
ENSG00000137802	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1061354	0.80[EUR][1000 genomes]
rs1081022	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070350	0.84[EUR][1000 genomes]
rs11634840	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11855017	0.84[ASN][1000 genomes]
rs11857301	0.92[ASN][1000 genomes]
rs1197666	0.83[EUR][1000 genomes]
rs1197670	0.84[EUR][1000 genomes]
rs1197704	0.99[ASN][1000 genomes]
rs1197768	0.84[ASN][1000 genomes]
rs1197769	0.84[ASN][1000 genomes]
rs1197772	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12441249	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1648827	0.84[EUR][1000 genomes]
rs1648828	0.84[EUR][1000 genomes]
rs1648829	0.84[EUR][1000 genomes]
rs1648830	0.84[EUR][1000 genomes]
rs1648831	0.84[EUR][1000 genomes]
rs1648832	0.84[EUR][1000 genomes]
rs1648833	0.84[EUR][1000 genomes]
rs1648834	0.84[EUR][1000 genomes]
rs1648835	0.84[EUR][1000 genomes]
rs1672464	0.84[EUR][1000 genomes]
rs1672465	0.84[EUR][1000 genomes]
rs1672466	0.84[EUR][1000 genomes]
rs16972089	0.92[ASN][1000 genomes]
rs1880937	0.81[ASN][1000 genomes]
rs1880938	0.84[ASN][1000 genomes]
rs1918314	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2250964	0.81[ASN][1000 genomes]
rs2577947	0.81[ASN][1000 genomes]
rs2577950	0.81[ASN][1000 genomes]
rs2577951	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577953	0.81[ASN][1000 genomes]
rs2577954	0.81[ASN][1000 genomes]
rs2577955	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2577958	0.84[ASN][1000 genomes]
rs2577959	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2605569	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605570	0.85[ASN][1000 genomes]
rs2695162	0.81[ASN][1000 genomes]
rs2695163	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2695164	0.81[ASN][1000 genomes]
rs2695165	0.88[ASN][1000 genomes]
rs2695166	0.84[ASN][1000 genomes]
rs2695169	0.81[ASN][1000 genomes]
rs2918051	0.81[ASN][1000 genomes]
rs2925337	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3784282	0.82[EUR][1000 genomes]
rs4078788	0.82[EUR][1000 genomes]
rs4371125	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57498313	0.84[EUR][1000 genomes]
rs7164209	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7165230	0.84[EUR][1000 genomes]
rs8028886	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8038783	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8039440	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs890508	0.84[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
rs2577952	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

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	chr15:42068200-42073600	Enhancers	HepG2	liver
5	chr15:42068200-42082600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:42068400-42073800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:42068400-42074600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:42068400-42075200	Weak transcription	Pancreas	Pancrea
9	chr15:42068400-42081800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:42068600-42073800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr15:42068600-42073800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr15:42068600-42081600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:42068800-42074400	Weak transcription	Primary B cells from cord blood	blood
14	chr15:42068800-42074400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr15:42069200-42075200	Weak transcription	K562	blood
16	chr15:42069400-42075200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:42069800-42075200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:42069800-42075200	Weak transcription	Gastric	stomach
19	chr15:42069800-42081800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:42070000-42081600	Weak transcription	Aorta	Aorta
21	chr15:42070000-42082600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr15:42070200-42109800	Weak transcription	Fetal Brain Male	brain
23	chr15:42070800-42075000	Weak transcription	Dnd41	blood
24	chr15:42071000-42074800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:42071000-42082400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:42071000-42082800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr15:42071000-42092800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:42071200-42074000	Enhancers	HUVEC	blood vessel
29	chr15:42071200-42074400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:42071200-42074600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:42071200-42092000	Weak transcription	Brain Germinal Matrix	brain
32	chr15:42071800-42073600	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr15:42072200-42074800	Weak transcription	Esophagus	oesophagus
34	chr15:42072400-42074400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr15:42072400-42074600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:42072400-42075600	Weak transcription	Lung	lung
37	chr15:42072400-42077400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:42072400-42080400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr15:42072400-42080800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr15:42072400-42081600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:42072600-42073600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:42072600-42075200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:42072600-42075200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr15:42072600-42075200	Weak transcription	HSMM	muscle
45	chr15:42072600-42080600	Weak transcription	Primary T cells from cord blood	blood
46	chr15:42072600-42081200	Weak transcription	HSMMtube	muscle
47	chr15:42072600-42081800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr15:42072600-42081800	Weak transcription	NH-A	brain
49	chr15:42072600-42082600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:42072800-42073800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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