Variant report

Variant	rs11633903
Chromosome Location	chr15:50577160-50577161
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50571295..50573619-chr15:50576803..50579324,3	MCF-7	breast:
2	chr10:58621047..58621938-chr15:50576510..50577380,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs10152534	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10220734	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10220755	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11070766	0.86[EUR][1000 genomes]
rs11070768	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs11629603	0.85[EUR][1000 genomes]
rs11630045	0.86[EUR][1000 genomes]
rs11631985	0.86[EUR][1000 genomes]
rs11632019	0.80[EUR][1000 genomes]
rs11632703	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs11636564	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs11637901	0.84[EUR][1000 genomes]
rs11638319	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]
rs11638432	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs11638564	0.85[EUR][1000 genomes]
rs11639406	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs11852487	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs11853236	0.85[EUR][1000 genomes]
rs11855823	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs12594956	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12901373	0.92[ASN][1000 genomes]
rs12902318	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs12910586	0.84[EUR][1000 genomes]
rs12912969	0.84[EUR][1000 genomes]
rs12913144	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1365504	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1645	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs16963604	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs16963612	0.85[EUR][1000 genomes]
rs17508371	0.86[EUR][1000 genomes]
rs1797311	0.88[CEU][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1972699	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2033115	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs2081628	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs2114447	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[ASN][1000 genomes]
rs28372114	0.84[EUR][1000 genomes]
rs28609286	0.85[EUR][1000 genomes]
rs28669213	0.85[EUR][1000 genomes]
rs28688566	0.84[EUR][1000 genomes]
rs28715646	0.84[EUR][1000 genomes]
rs28716586	0.86[EUR][1000 genomes]
rs28886692	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34197276	0.85[EUR][1000 genomes]
rs34590486	0.86[EUR][1000 genomes]
rs35000991	0.84[EUR][1000 genomes]
rs35024305	0.85[EUR][1000 genomes]
rs35168369	0.85[EUR][1000 genomes]
rs35777196	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3784297	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3985829	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4775874	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs4775875	0.86[EUR][1000 genomes]
rs4775876	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs4775877	0.84[EUR][1000 genomes]
rs489345	0.86[ASN][1000 genomes]
rs526045	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs535648	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62022573	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6493425	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493427	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493429	0.85[EUR][1000 genomes]
rs6493430	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7163457	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs7168233	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7173127	0.87[EUR][1000 genomes]
rs7176792	0.86[EUR][1000 genomes]
rs8025367	0.83[EUR][1000 genomes]
rs8026571	0.84[EUR][1000 genomes]
rs8026785	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8027367	0.85[EUR][1000 genomes]
rs8030036	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8031431	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8034615	0.84[EUR][1000 genomes]
rs8036354	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs8039829	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8041259	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8042451	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8042845	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8043257	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs11633903	CTD-3110H11.1	cis	Muscle Skeletal	GTEx
rs11633903	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs11633903	GABPB1-AS1	cis	lung	GTEx
rs11633903	GABPB2	cis	normal skin	skin_eQTL
rs11633903	GABPB2	cis	lesional skin	skin_eQTL
rs11633903	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs11633903	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs11633903	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs11633903	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs11633903	GABPB2	cis	uninvolved skin	skin_eQTL
rs11633903	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs11633903	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs11633903	CTD-3110H11.1	cis	Thyroid	GTEx
rs11633903	GABPB1-AS1	cis	Artery Tibial	GTEx
rs11633903	CTD-3110H11.1	cis	lung	GTEx
rs11633903	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs11633903	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs11633903	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50555400-50579400	Weak transcription	K562	blood
2	chr15:50566000-50580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:50567200-50579600	Weak transcription	Fetal Brain Female	brain
4	chr15:50567200-50579600	Weak transcription	Left Ventricle	heart
5	chr15:50567200-50579600	Weak transcription	Ovary	ovary
6	chr15:50567200-50580000	Weak transcription	Brain Germinal Matrix	brain
7	chr15:50567400-50579600	Weak transcription	Thymus	Thymus
8	chr15:50567600-50579600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr15:50567600-50579600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:50567600-50593000	Weak transcription	NHDF-Ad	bronchial
11	chr15:50567800-50579800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:50568000-50593400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:50568200-50579600	Weak transcription	Osteobl	bone
14	chr15:50568200-50592000	Weak transcription	NHLF	lung
15	chr15:50568400-50577600	Weak transcription	NH-A	brain
16	chr15:50568600-50579600	Weak transcription	Fetal Intestine Large	intestine
17	chr15:50568600-50580000	Weak transcription	Esophagus	oesophagus
18	chr15:50568800-50582000	Weak transcription	Stomach Mucosa	stomach
19	chr15:50568800-50591800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr15:50568800-50592200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:50568800-50599200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:50569000-50578600	Weak transcription	Fetal Muscle Leg	muscle
23	chr15:50569000-50579600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:50569200-50579600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:50569200-50579600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:50569200-50591800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:50569200-50592200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr15:50569800-50585400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:50570000-50577400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:50570000-50577800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:50570000-50591800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:50570200-50579600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:50570200-50591800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:50570400-50577800	Weak transcription	Placenta	Placenta
35	chr15:50570400-50579600	Weak transcription	Lung	lung
36	chr15:50570400-50580200	Weak transcription	Gastric	stomach
37	chr15:50570400-50606600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr15:50570800-50579600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr15:50570800-50579600	Weak transcription	Fetal Intestine Small	intestine
40	chr15:50570800-50591800	Weak transcription	HSMMtube	muscle
41	chr15:50570800-50600600	Weak transcription	Spleen	Spleen
42	chr15:50571000-50577600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:50571000-50592000	Weak transcription	Right Ventricle	heart
44	chr15:50571200-50579600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr15:50571200-50580000	Weak transcription	Brain Hippocampus Middle	brain
46	chr15:50571200-50593000	Weak transcription	Fetal Kidney	kidney
47	chr15:50572000-50589600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:50572400-50577600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr15:50572400-50579400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:50572600-50579400	Weak transcription	Primary T cells from cord blood	blood

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