Variant report

Variant	rs2577960
Chromosome Location	chr15:42028354-42028355
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42028222..42030756-chr15:42044005..42046072,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1107858	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11632424	0.88[EUR][1000 genomes]
rs11634956	0.92[ASN][1000 genomes]
rs11635067	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11635415	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11637341	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12440747	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12441300	0.81[EUR][1000 genomes]
rs1531140	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16971976	0.82[ASN][1000 genomes]
rs17677199	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17677991	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17678138	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17678552	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17678767	0.88[EUR][1000 genomes]
rs17734856	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1918310	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2004162	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2241522	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2277535	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2303516	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2303518	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2412622	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412641	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28373318	0.81[EUR][1000 genomes]
rs28401754	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28432037	0.81[EUR][1000 genomes]
rs28444909	0.87[EUR][1000 genomes]
rs28451764	0.81[EUR][1000 genomes]
rs28556632	0.82[ASN][1000 genomes]
rs28680296	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28701757	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28754734	0.89[EUR][1000 genomes]
rs28810086	0.82[ASN][1000 genomes]
rs28850384	0.82[ASN][1000 genomes]
rs3179542	0.86[ASN][1000 genomes]
rs3743024	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4923914	0.82[ASN][1000 genomes]
rs4923915	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4924570	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4924575	0.87[EUR][1000 genomes]
rs4924576	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62002066	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62002090	0.85[EUR][1000 genomes]
rs62002091	0.84[EUR][1000 genomes]
rs62003900	0.82[ASN][1000 genomes]
rs7171123	0.91[ASN][1000 genomes]
rs8025714	0.82[ASN][1000 genomes]
rs8035855	0.85[ASN][1000 genomes]
rs890498	0.81[EUR][1000 genomes]
rs890505	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9920903	0.90[EUR][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
rs2577960	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	chr15:42002200-42028400	Weak transcription	Pancreas	Pancrea
6	chr15:42003600-42028400	Weak transcription	Aorta	Aorta
7	chr15:42003800-42028400	Weak transcription	Gastric	stomach
8	chr15:42003800-42028400	Weak transcription	Small Intestine	intestine
9	chr15:42003800-42056000	Weak transcription	Colonic Mucosa	Colon
10	chr15:42005400-42028400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:42005800-42028400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:42006000-42028400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:42006200-42034800	Weak transcription	A549	lung
14	chr15:42006400-42041400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:42009800-42056800	Weak transcription	Fetal Heart	heart
16	chr15:42016000-42028400	Weak transcription	Psoas Muscle	Psoas
17	chr15:42017400-42062600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr15:42019000-42037000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:42019200-42037200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:42019400-42032800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr15:42019400-42036800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:42019400-42037000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr15:42019400-42060600	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr15:42020000-42036200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:42020400-42036200	Strong transcription	Fetal Thymus	thymus
26	chr15:42020600-42037000	Strong transcription	Hela-S3	cervix
27	chr15:42020800-42032600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr15:42020800-42033000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:42021000-42036800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:42021200-42029000	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr15:42021200-42032600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:42021200-42032800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:42021800-42028400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:42022400-42036800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:42022600-42033000	Strong transcription	Primary T cells from cord blood	blood
36	chr15:42022600-42034800	Weak transcription	Esophagus	oesophagus
37	chr15:42023200-42028400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:42023200-42028400	Weak transcription	Brain Angular Gyrus	brain
39	chr15:42023200-42035000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr15:42023400-42028400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:42023800-42031000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:42023800-42037000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:42023800-42037200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:42024000-42029200	Strong transcription	Primary B cells from cord blood	blood
45	chr15:42024000-42030400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr15:42024000-42036800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr15:42024000-42037000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr15:42024000-42037200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr15:42024400-42031200	Strong transcription	Fetal Intestine Small	intestine
50	chr15:42024400-42031200	Strong transcription	Fetal Lung	lung

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