Variant report

Variant	rs9524555
Chromosome Location	chr13:95259536-95259537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:95253610..95255807-chr13:95256426..95259673,3	MCF-7	breast:
2	chr13:95258888..95260648-chr13:95263620..95266096,2	K562	blood:
3	chr13:95258888..95261830-chr13:95264596..95266562,2	K562	blood:
4	chr13:95246788..95248667-chr13:95257874..95259560,2	MCF-7	breast:
5	chr13:95253721..95257093-chr13:95258270..95263356,4	K562	blood:

Variant related genes	Relation type
ENSG00000088451	Chromatin interaction
ENSG00000152749	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1112370	0.95[GIH][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1341267	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1408999	0.82[EUR][1000 genomes]
rs1572935	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2275648	0.81[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2298055	0.89[ASW][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2298056	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2298057	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs34350725	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34405130	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35253817	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742107	0.80[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3897473	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3897474	0.89[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4238308	0.96[ASN][1000 genomes]
rs4296139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4465476	0.90[ASN][1000 genomes]
rs4473052	0.82[EUR][1000 genomes]
rs4608209	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4771890	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4773801	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6492716	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6492718	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6492720	0.98[ASN][1000 genomes]
rs6492721	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6492723	0.96[ASN][1000 genomes]
rs6492725	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7321239	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7326576	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7330873	0.82[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7331814	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7339106	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7981788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7991607	0.80[EUR][1000 genomes]
rs7997035	0.81[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7997333	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7998025	0.81[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9301979	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]
rs9301981	0.84[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9301983	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9516437	0.84[CEU][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9516438	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9516440	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9516441	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9516443	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9516445	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9524544	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524545	0.81[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524547	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9524548	0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524549	0.81[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524550	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9524551	0.80[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9524553	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9524554	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9524556	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524560	0.90[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9524561	0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs9524562	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9524563	0.87[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9524566	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs9524568	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9556402	0.80[CEU][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9556405	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9561641	0.82[TSI][hapmap]
rs9561642	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9561643	0.91[ASN][1000 genomes]
rs9561645	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9590037	0.88[AMR][1000 genomes];0.90[EUR][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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9524555	GPR180	cis	parietal	SCAN
rs9524555	GPR180	cis	Esophagus Mucosa	GTEx
rs9524555	GPR180	cis	Muscle Skeletal	GTEx
rs9524555	GPR180	cis	Skin Sun Exposed Lower leg	GTEx
rs9524555	GPR180	cis	Artery Tibial	GTEx
rs9524555	GPR180	cis	Adipose Subcutaneous	GTEx
rs9524555	GPR180	cis	Stomach	GTEx
rs9524555	GPR180	cis	lung	GTEx
rs9524555	GPR180	cis	Whole Blood	GTEx
rs9524555	ZDHHC9	trans	parietal	SCAN
rs9524555	GPR180	cis	cerebellum	SCAN
rs9524555	GPR180	cis	Nerve Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95254600-95276600	Weak transcription	Small Intestine	intestine
2	chr13:95254600-95284000	Weak transcription	Spleen	Spleen
3	chr13:95254800-95263000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr13:95254800-95263800	Weak transcription	Left Ventricle	heart
5	chr13:95254800-95263800	Weak transcription	Pancreas	Pancrea
6	chr13:95254800-95263800	Weak transcription	Psoas Muscle	Psoas
7	chr13:95254800-95268200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr13:95254800-95272000	Weak transcription	Lung	lung
9	chr13:95254800-95275400	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr13:95254800-95275600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr13:95254800-95288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:95255000-95260200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:95255000-95260400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr13:95255000-95262800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr13:95255000-95262800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr13:95255000-95263200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr13:95255000-95263200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr13:95255000-95275400	Weak transcription	Aorta	Aorta
19	chr13:95255000-95275600	Weak transcription	Right Ventricle	heart
20	chr13:95255000-95276200	Weak transcription	HSMMtube	muscle
21	chr13:95255000-95281000	Weak transcription	Colonic Mucosa	Colon
22	chr13:95255200-95262000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr13:95255200-95262800	Weak transcription	Fetal Kidney	kidney
24	chr13:95255200-95272200	Weak transcription	Colon Smooth Muscle	Colon
25	chr13:95255200-95276200	Weak transcription	Fetal Brain Female	brain
26	chr13:95255200-95278200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr13:95255200-95282200	Weak transcription	Brain Angular Gyrus	brain
28	chr13:95255400-95288600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr13:95255600-95268000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr13:95255600-95281800	Weak transcription	Fetal Brain Male	brain
31	chr13:95255600-95282600	Weak transcription	Fetal Heart	heart
32	chr13:95255800-95259600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr13:95255800-95259800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr13:95255800-95259800	Weak transcription	Brain Anterior Caudate	brain
35	chr13:95255800-95260400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr13:95255800-95260400	Weak transcription	Brain Substantia Nigra	brain
37	chr13:95255800-95261600	Weak transcription	Primary T cells from cord blood	blood
38	chr13:95255800-95263600	Weak transcription	Fetal Intestine Small	intestine
39	chr13:95255800-95264400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr13:95255800-95268000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr13:95255800-95278000	Weak transcription	Hela-S3	cervix
42	chr13:95255800-95284000	Weak transcription	K562	blood
43	chr13:95255800-95285000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr13:95256400-95262800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr13:95256600-95272000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr13:95257000-95262800	Weak transcription	Thymus	Thymus
47	chr13:95257000-95263800	Weak transcription	Esophagus	oesophagus
48	chr13:95257400-95259800	Genic enhancers	Dnd41	blood
49	chr13:95257400-95260000	Strong transcription	Fetal Thymus	thymus
50	chr13:95257400-95260400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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