Variant report

Variant	rs3985829
Chromosome Location	chr15:50569035-50569036
allele	A/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:50567739..50569833-chr15:50605430..50607848,2	MCF-7	breast:
2	chr15:50567278..50569331-chr15:50646993..50649924,2	K562	blood:
3	chr15:50563105..50566724-chr15:50567713..50571020,4	K562	blood:
4	chr15:50563105..50565839-chr15:50567791..50570281,2	K562	blood:
5	chr15:50561224..50565664-chr15:50565813..50569433,4	MCF-7	breast:
6	chr15:50559504..50561067-chr15:50567809..50570782,2	K562	blood:
7	chr15:50559536..50561689-chr15:50567895..50570297,2	K562	blood:
8	chr15:50489080..50491819-chr15:50568485..50571202,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000244879	Chromatin interaction
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10152534	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10220734	0.92[ASN][1000 genomes]
rs10220740	0.91[EUR][1000 genomes]
rs10220755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633903	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11638319	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12594956	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12901373	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913144	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1365503	0.91[EUR][1000 genomes]
rs1365504	0.95[ASN][1000 genomes]
rs1797311	0.86[YRI][hapmap]
rs1972699	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[ASN][1000 genomes]
rs2114447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2187576	0.81[EUR][1000 genomes]
rs28886692	0.93[ASN][1000 genomes]
rs35777196	0.93[ASN][1000 genomes]
rs3784296	0.91[EUR][1000 genomes]
rs3784297	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs489345	0.89[ASN][1000 genomes]
rs535648	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs62022573	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6493425	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6493427	1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6493430	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7168233	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs8026785	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8030036	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8031431	0.92[ASN][1000 genomes]
rs8039829	0.93[ASN][1000 genomes]
rs8041259	0.94[ASN][1000 genomes]
rs8042451	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs8042845	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs8043257	0.87[AFR][1000 genomes];0.95[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs3985829	GABPB1-AS1	cis	Artery Tibial	GTEx
rs3985829	GABPB1-AS1	cis	lung	GTEx
rs3985829	CTD-3110H11.1	cis	Artery Tibial	GTEx
rs3985829	GABPB1-AS1	cis	Artery Aorta	GTEx
rs3985829	GABPB1-AS1	cis	Esophagus Mucosa	GTEx
rs3985829	GABPB1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs3985829	GABPB1-AS1	cis	Adipose Subcutaneous	GTEx
rs3985829	CTD-3110H11.1	cis	lung	GTEx
rs3985829	CTD-3110H11.1	cis	Nerve Tibial	GTEx
rs3985829	CTD-3110H11.1	cis	Esophagus Mucosa	GTEx
rs3985829	CTD-3110H11.1	cis	Esophagus Muscularis	GTEx
rs3985829	GABPB1-AS1	cis	Nerve Tibial	GTEx
rs3985829	CTD-3110H11.1	cis	Skin Sun Exposed Lower leg	GTEx
rs3985829	CTD-3110H11.1	cis	Artery Aorta	GTEx
rs3985829	CTD-3110H11.1	cis	Adipose Subcutaneous	GTEx
rs3985829	GABPB1-AS1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50555400-50579400	Weak transcription	K562	blood
2	chr15:50558000-50572400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:50558600-50569800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:50564000-50574400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr15:50564200-50572400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:50564600-50569600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:50566000-50576200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:50566000-50580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:50566400-50576400	Weak transcription	HUVEC	blood vessel
10	chr15:50566600-50572000	Weak transcription	NHEK	skin
11	chr15:50566800-50569800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:50567000-50569400	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr15:50567200-50569800	Weak transcription	Primary T cells from cord blood	blood
14	chr15:50567200-50576200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:50567200-50579600	Weak transcription	Fetal Brain Female	brain
16	chr15:50567200-50579600	Weak transcription	Left Ventricle	heart
17	chr15:50567200-50579600	Weak transcription	Ovary	ovary
18	chr15:50567200-50580000	Weak transcription	Brain Germinal Matrix	brain
19	chr15:50567400-50570600	Weak transcription	Fetal Thymus	thymus
20	chr15:50567400-50579600	Weak transcription	Thymus	Thymus
21	chr15:50567600-50579600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:50567600-50579600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:50567600-50593000	Weak transcription	NHDF-Ad	bronchial
24	chr15:50567800-50569600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:50567800-50579800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr15:50568000-50569600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:50568000-50569600	Enhancers	Primary B cells from cord blood	blood
28	chr15:50568000-50593400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr15:50568200-50571000	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr15:50568200-50572400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr15:50568200-50576200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:50568200-50579600	Weak transcription	Osteobl	bone
33	chr15:50568200-50592000	Weak transcription	NHLF	lung
34	chr15:50568400-50571800	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr15:50568400-50576000	Weak transcription	Liver	Liver
36	chr15:50568400-50576000	Weak transcription	HSMM	muscle
37	chr15:50568400-50577600	Weak transcription	NH-A	brain
38	chr15:50568600-50569400	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr15:50568600-50579600	Weak transcription	Fetal Intestine Large	intestine
40	chr15:50568600-50580000	Weak transcription	Esophagus	oesophagus
41	chr15:50568800-50570000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:50568800-50570600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:50568800-50572400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:50568800-50576000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr15:50568800-50582000	Weak transcription	Stomach Mucosa	stomach
46	chr15:50568800-50591800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr15:50568800-50592200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr15:50568800-50599200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr15:50569000-50576200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:50569000-50576200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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