Variant report

Variant	rs11638319
Chromosome Location	chr15:50606752-50606753
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50604955..50607195-chr15:50647798..50650505,2	MCF-7	breast:
2	chr15:50604584..50606949-chr15:50645363..50647789,2	MCF-7	breast:
3	chr15:50473845..50474779-chr15:50606266..50607223,10	MCF-7	breast:
4	chr15:50554233..50555022-chr15:50605935..50606770,2	MCF-7	breast:
5	chr15:50606397..50607189-chr9:112084217..112084875,2	MCF-7	breast:
6	chr15:50440291..50441191-chr15:50605962..50607640,5	MCF-7	breast:
7	chr15:50480774..50483234-chr15:50605511..50608166,2	K562	blood:
8	chr15:50606170..50608244-chr15:50645092..50648009,4	MCF-7	breast:
9	chr15:50597253..50599455-chr15:50605376..50607840,2	K562	blood:
10	chr15:50440216..50441453-chr15:50606385..50608916,26	MCF-7	breast:
11	chr15:50440355..50443331-chr15:50606446..50609339,3	MCF-7	breast:
12	chr15:50481734..50484322-chr15:50606666..50608276,2	K562	blood:
13	chr15:50567739..50569833-chr15:50605430..50607848,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000140284	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000244879	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10152534	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10220734	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10220755	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11070766	0.85[EUR][1000 genomes]
rs11070768	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs11629603	0.84[EUR][1000 genomes]
rs11630045	0.85[EUR][1000 genomes]
rs11631985	0.85[EUR][1000 genomes]
rs11632019	0.80[EUR][1000 genomes]
rs11632703	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs11633903	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11636564	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs11637901	0.83[EUR][1000 genomes]
rs11638432	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs11638564	0.85[EUR][1000 genomes]
rs11639406	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs11852487	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs11853236	0.84[EUR][1000 genomes]
rs11855823	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs12594956	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901373	0.97[ASN][1000 genomes]
rs12902318	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs12910586	0.84[EUR][1000 genomes]
rs12912969	0.83[EUR][1000 genomes]
rs12913144	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1365504	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1645	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs16963604	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs16963612	0.85[EUR][1000 genomes]
rs17508371	0.85[EUR][1000 genomes]
rs1797311	0.90[CEU][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1972699	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033115	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs2081628	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs2114447	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28372114	0.84[EUR][1000 genomes]
rs28609286	0.84[EUR][1000 genomes]
rs28669213	0.84[EUR][1000 genomes]
rs28688566	0.83[EUR][1000 genomes]
rs28715646	0.83[EUR][1000 genomes]
rs28716586	0.85[EUR][1000 genomes]
rs28886692	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34197276	0.84[EUR][1000 genomes]
rs34590486	0.85[EUR][1000 genomes]
rs35000991	0.84[EUR][1000 genomes]
rs35024305	0.84[EUR][1000 genomes]
rs35168369	0.84[EUR][1000 genomes]
rs35777196	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784297	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3985829	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4775874	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs4775875	0.85[EUR][1000 genomes]
rs4775876	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs4775877	0.84[EUR][1000 genomes]
rs489345	0.92[ASN][1000 genomes]
rs526045	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs535648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62022573	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493425	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493427	0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493429	0.84[EUR][1000 genomes]
rs6493430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7163457	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs7168233	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7173127	0.84[EUR][1000 genomes]
rs7176792	0.85[EUR][1000 genomes]
rs8025367	0.82[EUR][1000 genomes]
rs8026571	0.83[EUR][1000 genomes]
rs8026785	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8027367	0.84[EUR][1000 genomes]
rs8030036	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8031431	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8034615	0.83[EUR][1000 genomes]
rs8036354	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs8039829	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8041259	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8042451	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8042845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8043257	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs11638319	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs11638319	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs11638319	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs11638319	CTD-3110H11.1	cis	Thyroid	GTEx
rs11638319	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs11638319	CTD-3110H11.1	cis	lung	GTEx
rs11638319	GABPB2	cis	normal skin	skin_eQTL
rs11638319	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs11638319	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11638319	GABPB2	cis	uninvolved skin	skin_eQTL
rs11638319	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs11638319	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs11638319	GABPB2	cis	lesional skin	skin_eQTL
rs11638319	GABPB1-AS1	cis	Artery Aorta	GTEx
rs11638319	GABPB1-AS1	cis	lung	GTEx
rs11638319	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs11638319	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs11638319	GABPB1-AS1	cis	Artery Tibial	GTEx
rs11638319	CTD-3110H11.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50580800-50638400	Weak transcription	NHEK	skin
2	chr15:50594000-50608400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr15:50594000-50610200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:50594200-50608400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:50594600-50610400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:50596400-50623400	Weak transcription	Aorta	Aorta
7	chr15:50596600-50608000	Weak transcription	Liver	Liver
8	chr15:50596800-50611400	Weak transcription	Right Atrium	heart
9	chr15:50597000-50628600	Weak transcription	Fetal Stomach	stomach
10	chr15:50600600-50610400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:50600600-50610400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:50600800-50607800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:50600800-50608000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:50600800-50608200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:50600800-50608200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:50600800-50608200	Weak transcription	Adipose Nuclei	Adipose
17	chr15:50600800-50608200	Weak transcription	Hela-S3	cervix
18	chr15:50600800-50610200	Weak transcription	Primary T cells from cord blood	blood
19	chr15:50600800-50610200	Weak transcription	Pancreas	Pancrea
20	chr15:50600800-50610400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr15:50600800-50610600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:50600800-50610800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:50600800-50610800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr15:50600800-50612800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr15:50600800-50613600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:50600800-50617200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:50600800-50618600	Weak transcription	Fetal Intestine Large	intestine
28	chr15:50600800-50623200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:50600800-50629400	Weak transcription	Placenta	Placenta
30	chr15:50600800-50631200	Weak transcription	Left Ventricle	heart
31	chr15:50600800-50635400	Weak transcription	HepG2	liver
32	chr15:50600800-50641400	Weak transcription	HSMM	muscle
33	chr15:50600800-50641600	Weak transcription	Fetal Kidney	kidney
34	chr15:50600800-50643000	Weak transcription	Fetal Thymus	thymus
35	chr15:50600800-50643400	Weak transcription	Fetal Muscle Leg	muscle
36	chr15:50600800-50644200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:50600800-50644600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:50601000-50606800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr15:50601000-50607800	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr15:50601000-50608000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:50601000-50610200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:50601000-50610400	Weak transcription	Primary B cells from cord blood	blood
43	chr15:50601000-50610400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr15:50601000-50610800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:50601000-50614400	Weak transcription	Psoas Muscle	Psoas
46	chr15:50601000-50622800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:50601000-50627200	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr15:50601000-50630400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr15:50601000-50637000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:50601000-50638400	Weak transcription	HUVEC	blood vessel

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