Variant report

Variant	rs2577950
Chromosome Location	chr15:42032655-42032656
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	chr15:42030668..42033706-chr15:42033784..42035660,3	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1008710	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs10152332	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10152364	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10775122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs10775123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10775124	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1081022	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11070345	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11632100	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11634840	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11855017	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1197666	1.00[CEU][hapmap]
rs1197670	0.81[ASN][1000 genomes]
rs1197704	0.85[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs1197768	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1197769	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1197772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12148330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12441249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900295	0.81[EUR][1000 genomes]
rs12915325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12916992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1648830	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1648833	1.00[CEU][hapmap]
rs1648834	1.00[CEU][hapmap]
rs1648835	1.00[CEU][hapmap]
rs1672465	1.00[CEU][hapmap]
rs1672466	1.00[CEU][hapmap]
rs16972089	0.93[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs16972136	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs1867416	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1867417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880937	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880938	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1899819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1899820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1899821	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[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];0.84[LWK][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2009310	0.85[ASN][1000 genomes]
rs2141141	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2178004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2250964	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2577952	0.81[ASN][1000 genomes]
rs2577953	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577955	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577958	0.98[AMR][1000 genomes];0.95[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];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2605569	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2605570	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2695162	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695163	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]
rs2695164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695166	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2695168	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2695169	0.92[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695170	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2918051	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2925337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2950446	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4244585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4270151	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4371125	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4465584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4923908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924568	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924571	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4924572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62002069	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493008	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493010	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7164209	0.93[ASN][1000 genomes]
rs7169496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169668	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7176474	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7177911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8027390	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8028886	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8030179	0.83[ASN][1000 genomes]
rs8034261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8038148	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8038783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8039440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2577950	MGA	Cis_1M	lymphoblastoid	RTeQTL
rs2577950	C17orf85	trans	parietal	SCAN

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	chr15:42003800-42056000	Weak transcription	Colonic Mucosa	Colon
6	chr15:42006200-42034800	Weak transcription	A549	lung
7	chr15:42006400-42041400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:42009800-42056800	Weak transcription	Fetal Heart	heart
9	chr15:42017400-42062600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr15:42019000-42037000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:42019200-42037200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:42019400-42032800	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr15:42019400-42036800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:42019400-42037000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:42019400-42060600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr15:42020000-42036200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:42020400-42036200	Strong transcription	Fetal Thymus	thymus
18	chr15:42020600-42037000	Strong transcription	Hela-S3	cervix
19	chr15:42020800-42033000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:42021000-42036800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr15:42021200-42032800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:42022400-42036800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:42022600-42033000	Strong transcription	Primary T cells from cord blood	blood
24	chr15:42022600-42034800	Weak transcription	Esophagus	oesophagus
25	chr15:42023200-42035000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr15:42023800-42037000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:42023800-42037200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:42024000-42036800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr15:42024000-42037000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr15:42024000-42037200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr15:42024400-42032800	Strong transcription	Fetal Stomach	stomach
32	chr15:42024600-42037000	Strong transcription	Placenta	Placenta
33	chr15:42025000-42033200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:42025000-42034800	Weak transcription	NHLF	lung
35	chr15:42025000-42045800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:42025200-42036000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:42025200-42065400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr15:42025400-42037200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:42025600-42037000	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:42025800-42045000	Weak transcription	Stomach Mucosa	stomach
41	chr15:42026000-42033200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:42026400-42035600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:42027000-42037800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:42027200-42033200	Strong transcription	GM12878-XiMat	blood
45	chr15:42028800-42034600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:42028800-42041200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr15:42029000-42033800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr15:42029000-42034200	Weak transcription	Pancreas	Pancrea
49	chr15:42029000-42034600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr15:42029000-42034600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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