Variant report

Variant	rs1572935
Chromosome Location	chr13:95272552-95272553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95272285..95273035-chr13:96056279..96056904,2	K562	blood:
2	chr13:95272320..95273164-chr13:95808439..95809049,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1112370	0.91[GIH][hapmap]
rs1341267	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2298055	0.81[ASW][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2298056	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2298057	1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35253817	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3897473	0.96[ASN][1000 genomes]
rs3897474	0.93[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4238308	0.99[ASN][1000 genomes]
rs4296139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4465476	0.92[ASN][1000 genomes]
rs4771890	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6492720	0.95[ASN][1000 genomes]
rs6492721	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6492723	0.99[ASN][1000 genomes]
rs6492725	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7326576	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7330873	0.90[MEX][hapmap]
rs7981788	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7997035	0.86[GIH][hapmap];0.86[MEX][hapmap]
rs7998025	0.81[GIH][hapmap]
rs9301979	0.81[GIH][hapmap];0.86[MEX][hapmap]
rs9301981	0.86[YRI][hapmap]
rs9516443	0.81[YRI][hapmap];0.81[AFR][1000 genomes]
rs9516445	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9516448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524545	0.81[GIH][hapmap];0.86[MEX][hapmap]
rs9524549	0.81[GIH][hapmap];0.86[MEX][hapmap]
rs9524555	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]
rs9524556	0.98[ASN][1000 genomes]
rs9524557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9524559	0.95[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9524560	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9524561	1.00[CEU][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9524562	0.94[CEU][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9524563	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9524566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524568	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9556402	0.83[GIH][hapmap];0.86[MEX][hapmap]
rs9556405	0.94[ASN][1000 genomes]
rs9561643	0.88[ASN][1000 genomes]
rs9561645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1572935	GPR180	cis	cerebellum	SCAN
rs1572935	GPR180	cis	lung	GTEx
rs1572935	GPR180	cis	Nerve Tibial	GTEx
rs1572935	GPR180	cis	parietal	SCAN
rs1572935	CLDN10	cis	cerebellum	SCAN
rs1572935	GPR180	cis	Muscle Skeletal	GTEx

Chromatin state (count:120 , 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	chr13:95254800-95275400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr13:95254800-95275600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:95254800-95288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:95255000-95275400	Weak transcription	Aorta	Aorta
7	chr13:95255000-95275600	Weak transcription	Right Ventricle	heart
8	chr13:95255000-95276200	Weak transcription	HSMMtube	muscle
9	chr13:95255000-95281000	Weak transcription	Colonic Mucosa	Colon
10	chr13:95255200-95276200	Weak transcription	Fetal Brain Female	brain
11	chr13:95255200-95278200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr13:95255200-95282200	Weak transcription	Brain Angular Gyrus	brain
13	chr13:95255400-95288600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr13:95255600-95281800	Weak transcription	Fetal Brain Male	brain
15	chr13:95255600-95282600	Weak transcription	Fetal Heart	heart
16	chr13:95255800-95278000	Weak transcription	Hela-S3	cervix
17	chr13:95255800-95284000	Weak transcription	K562	blood
18	chr13:95255800-95285000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr13:95259000-95275400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr13:95259600-95275400	Weak transcription	Primary B cells from cord blood	blood
21	chr13:95259600-95275400	Weak transcription	Brain Hippocampus Middle	brain
22	chr13:95259800-95275800	Weak transcription	Gastric	stomach
23	chr13:95259800-95276000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr13:95259800-95282000	Weak transcription	Brain Germinal Matrix	brain
25	chr13:95260000-95285800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr13:95261800-95275400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr13:95262200-95278200	Weak transcription	Brain Substantia Nigra	brain
28	chr13:95263600-95276200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr13:95264000-95275400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr13:95264000-95275400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr13:95264000-95284000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr13:95264200-95275400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr13:95264200-95275400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr13:95264200-95275400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr13:95264200-95275400	Weak transcription	Ovary	ovary
36	chr13:95264200-95275400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr13:95264200-95280200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr13:95264200-95299600	Weak transcription	Psoas Muscle	Psoas
39	chr13:95264400-95275400	Weak transcription	Placenta	Placenta
40	chr13:95264600-95275200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr13:95264600-95275400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr13:95264600-95282400	Weak transcription	Pancreas	Pancrea
43	chr13:95264600-95289200	Weak transcription	Esophagus	oesophagus
44	chr13:95264600-95289600	Weak transcription	Fetal Kidney	kidney
45	chr13:95264800-95275200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr13:95264800-95284600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr13:95265400-95286800	Weak transcription	A549	lung
48	chr13:95265600-95275400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr13:95265600-95293400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr13:95265800-95275400	Weak transcription	HSMM	muscle

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