Variant report

Variant	rs4489873
Chromosome Location	chr13:95242527-95242528
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:95239604..95244958-chr13:95245816..95249752,6	K562	blood:
2	chr13:95242026..95244794-chr13:95245664..95248411,3	MCF-7	breast:
3	chr13:95242101..95243874-chr13:95245900..95247690,2	K562	blood:

Variant related genes	Relation type
ENSG00000088451	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1112370	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs1408999	0.96[ASN][1000 genomes]
rs2275647	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275648	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs2298058	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34350725	1.00[ASN][1000 genomes]
rs34405130	1.00[ASN][1000 genomes]
rs35678857	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742107	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs4296139	0.85[YRI][hapmap]
rs4473052	0.96[ASN][1000 genomes]
rs4608209	0.97[ASN][1000 genomes]
rs4773801	1.00[ASN][1000 genomes]
rs6492716	1.00[ASN][1000 genomes]
rs6492717	0.91[ASN][1000 genomes]
rs6492718	1.00[ASN][1000 genomes]
rs7321239	1.00[ASN][1000 genomes]
rs7330873	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs7331814	0.99[ASN][1000 genomes]
rs7339106	1.00[ASN][1000 genomes]
rs7991607	1.00[ASN][1000 genomes]
rs7997035	0.90[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7997333	1.00[ASN][1000 genomes]
rs7998025	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs9301979	0.90[CHB][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs9301981	0.85[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs9301983	0.96[ASN][1000 genomes]
rs9516434	0.85[ASN][1000 genomes]
rs9516437	0.90[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs9516438	0.95[ASN][1000 genomes]
rs9516440	0.96[ASN][1000 genomes]
rs9516441	0.94[ASN][1000 genomes]
rs9516443	0.85[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs9524544	0.89[CHB][hapmap];0.83[JPT][hapmap];0.99[ASN][1000 genomes]
rs9524545	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs9524547	0.99[ASN][1000 genomes]
rs9524548	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs9524549	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs9524550	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs9524551	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs9524553	0.96[ASN][1000 genomes]
rs9524554	0.96[ASN][1000 genomes]
rs9556402	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs9556403	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9561636	1.00[ASW][hapmap];0.88[MKK][hapmap]
rs9561638	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9561642	0.96[ASN][1000 genomes]
rs9561643	0.80[AMR][1000 genomes]
rs9590037	0.99[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	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832685	chr13:95179676-95279966	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv832686	chr13:95206742-95400992	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4489873	GPR180	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95219600-95245600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr13:95221400-95242800	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr13:95221400-95245800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr13:95222000-95245000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr13:95222000-95247200	Weak transcription	Fetal Brain Male	brain
6	chr13:95222200-95245000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr13:95222200-95245200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr13:95223000-95245800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr13:95224200-95246400	Weak transcription	Fetal Heart	heart
10	chr13:95224200-95246400	Weak transcription	Stomach Mucosa	stomach
11	chr13:95224400-95242800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr13:95225000-95247400	Weak transcription	Fetal Brain Female	brain
13	chr13:95225200-95242800	Weak transcription	Small Intestine	intestine
14	chr13:95226000-95245800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr13:95226200-95245400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr13:95226800-95246800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr13:95233000-95246600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr13:95233200-95242800	Weak transcription	NHEK	skin
19	chr13:95233200-95246600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr13:95233200-95247000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr13:95233400-95247600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr13:95233800-95242800	Weak transcription	Brain Substantia Nigra	brain
23	chr13:95234200-95244600	Weak transcription	Esophagus	oesophagus
24	chr13:95234400-95246800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr13:95234400-95246800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr13:95234400-95247000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr13:95234600-95247200	Weak transcription	Lung	lung
28	chr13:95234800-95246400	Weak transcription	Colon Smooth Muscle	Colon
29	chr13:95235000-95246800	Weak transcription	Spleen	Spleen
30	chr13:95235200-95243600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr13:95235200-95246400	Weak transcription	Brain Anterior Caudate	brain
32	chr13:95235200-95246600	Weak transcription	Psoas Muscle	Psoas
33	chr13:95235200-95246800	Weak transcription	Right Ventricle	heart
34	chr13:95235200-95247000	Weak transcription	Ovary	ovary
35	chr13:95235200-95247400	Weak transcription	Gastric	stomach
36	chr13:95235400-95242800	Weak transcription	Colonic Mucosa	Colon
37	chr13:95235400-95246400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr13:95235400-95246400	Weak transcription	Brain Hippocampus Middle	brain
39	chr13:95235600-95242600	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr13:95235600-95243200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr13:95235600-95243600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr13:95235600-95244000	Weak transcription	Fetal Kidney	kidney
43	chr13:95235600-95246800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr13:95235600-95246800	Weak transcription	Pancreas	Pancrea
45	chr13:95235600-95247000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr13:95235600-95247400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr13:95235600-95247400	Weak transcription	Aorta	Aorta
48	chr13:95235600-95247400	Weak transcription	HSMMtube	muscle
49	chr13:95235800-95243000	Weak transcription	Thymus	Thymus
50	chr13:95236000-95242600	Weak transcription	HMEC	breast

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