Variant report

Variant	rs9301979
Chromosome Location	chr13:95243270-95243271
allele	A/G
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	chr13:95242784..95245986-chr13:95246161..95249973,6	MCF-7	breast:
3	chr13:95242026..95244794-chr13:95245664..95248411,3	MCF-7	breast:
4	chr13:95242101..95243874-chr13:95245900..95247690,2	K562	blood:

Variant related genes	Relation type
ENSG00000088451	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1112370	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1408999	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1572935	0.81[GIH][hapmap];0.86[MEX][hapmap]
rs2275647	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs2275648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298055	0.89[ASW][hapmap]
rs2298058	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs34350725	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34405130	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35253817	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35678857	0.98[ASN][1000 genomes]
rs3742107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3897473	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3897474	0.89[ASW][hapmap];0.88[CEU][hapmap];0.80[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4473052	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4489873	0.90[CHB][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs4608209	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4773801	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492716	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492717	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6492718	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7321239	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7330873	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7331814	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7339106	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7981788	0.81[CEU][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7991607	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7997035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7997333	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7998025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9301981	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9301983	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9516434	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9516437	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9516438	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9516440	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9516441	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9516443	0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9516445	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524544	1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9524545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524547	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524548	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524553	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9524554	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9524555	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[GIH][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524556	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524557	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524559	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[GIH][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9556402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9556403	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs9556405	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9561638	0.99[ASN][1000 genomes]
rs9561641	0.86[TSI][hapmap]
rs9561642	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9590037	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9301979	GPR180	cis	lung	GTEx
rs9301979	GPR180	cis	Adipose Subcutaneous	GTEx
rs9301979	GPR180	cis	parietal	SCAN
rs9301979	GPR180	cis	Artery Tibial	GTEx
rs9301979	GPR180	cis	Whole Blood	GTEx
rs9301979	GPR180	cis	Esophagus Mucosa	GTEx
rs9301979	GPR180	cis	Stomach	GTEx
rs9301979	GPC5	cis	parietal	SCAN
rs9301979	GPR180	cis	cerebellum	SCAN
rs9301979	GPR180	cis	Nerve Tibial	GTEx
rs9301979	GPR180	cis	Muscle Skeletal	GTEx
rs9301979	GPR180	cis	Skin Sun Exposed Lower leg	GTEx
rs9301979	ZDHHC9	trans	parietal	SCAN

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	chr13:95221400-95245800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr13:95222000-95245000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr13:95222000-95247200	Weak transcription	Fetal Brain Male	brain
5	chr13:95222200-95245000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr13:95222200-95245200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr13:95223000-95245800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr13:95224200-95246400	Weak transcription	Fetal Heart	heart
9	chr13:95224200-95246400	Weak transcription	Stomach Mucosa	stomach
10	chr13:95225000-95247400	Weak transcription	Fetal Brain Female	brain
11	chr13:95226000-95245800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr13:95226200-95245400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr13:95226800-95246800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr13:95233000-95246600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr13:95233200-95246600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr13:95233200-95247000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr13:95233400-95247600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr13:95234200-95244600	Weak transcription	Esophagus	oesophagus
19	chr13:95234400-95246800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr13:95234400-95246800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr13:95234400-95247000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr13:95234600-95247200	Weak transcription	Lung	lung
23	chr13:95234800-95246400	Weak transcription	Colon Smooth Muscle	Colon
24	chr13:95235000-95246800	Weak transcription	Spleen	Spleen
25	chr13:95235200-95243600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr13:95235200-95246400	Weak transcription	Brain Anterior Caudate	brain
27	chr13:95235200-95246600	Weak transcription	Psoas Muscle	Psoas
28	chr13:95235200-95246800	Weak transcription	Right Ventricle	heart
29	chr13:95235200-95247000	Weak transcription	Ovary	ovary
30	chr13:95235200-95247400	Weak transcription	Gastric	stomach
31	chr13:95235400-95246400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr13:95235400-95246400	Weak transcription	Brain Hippocampus Middle	brain
33	chr13:95235600-95243600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr13:95235600-95244000	Weak transcription	Fetal Kidney	kidney
35	chr13:95235600-95246800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr13:95235600-95246800	Weak transcription	Pancreas	Pancrea
37	chr13:95235600-95247000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr13:95235600-95247400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr13:95235600-95247400	Weak transcription	Aorta	Aorta
40	chr13:95235600-95247400	Weak transcription	HSMMtube	muscle
41	chr13:95236600-95246400	Weak transcription	Brain Angular Gyrus	brain
42	chr13:95236600-95246600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr13:95237000-95246000	Weak transcription	A549	lung
44	chr13:95237000-95246400	Weak transcription	NHLF	lung
45	chr13:95237200-95245800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr13:95237600-95243600	Weak transcription	HUVEC	blood vessel
47	chr13:95237600-95244000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr13:95237600-95246600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr13:95237600-95246800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr13:95237800-95246400	Weak transcription	Primary hematopoietic stem cells	blood

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