Variant report

Variant	rs2298055
Chromosome Location	chr13:95281296-95281297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95279700..95282385-chr13:95284753..95286898,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1341267	0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1572935	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	0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2298057	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35253817	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3897473	0.91[ASN][1000 genomes]
rs3897474	0.87[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4238308	0.93[ASN][1000 genomes]
rs4296139	0.87[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4465476	0.98[ASN][1000 genomes]
rs4771890	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492720	0.90[ASN][1000 genomes]
rs6492721	0.82[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6492723	0.93[ASN][1000 genomes]
rs6492725	0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7326576	0.87[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7981788	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9301979	0.89[ASW][hapmap]
rs9301981	1.00[YRI][hapmap]
rs9301983	0.84[AFR][1000 genomes]
rs9516437	0.81[YRI][hapmap]
rs9516443	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs9516445	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9516448	0.87[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9516450	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9524554	0.83[AFR][1000 genomes]
rs9524555	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]
rs9524556	0.94[ASN][1000 genomes]
rs9524557	0.92[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9524559	0.89[ASW][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9524560	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9524561	0.80[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9524562	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9524563	0.97[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9524566	0.80[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524568	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9556405	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9561643	0.84[ASN][1000 genomes]
rs9561645	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2298055	GPR180	cis	parietal	SCAN
rs2298055	GPR180	cis	Nerve Tibial	GTEx
rs2298055	GPR180	cis	cerebellum	SCAN
rs2298055	CLDN10	cis	cerebellum	SCAN
rs2298055	GPR180	cis	Muscle Skeletal	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95254600-95284000	Weak transcription	Spleen	Spleen
2	chr13:95254800-95288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:95255200-95282200	Weak transcription	Brain Angular Gyrus	brain
4	chr13:95255400-95288600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr13:95255600-95281800	Weak transcription	Fetal Brain Male	brain
6	chr13:95255600-95282600	Weak transcription	Fetal Heart	heart
7	chr13:95255800-95284000	Weak transcription	K562	blood
8	chr13:95255800-95285000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr13:95259800-95282000	Weak transcription	Brain Germinal Matrix	brain
10	chr13:95260000-95285800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:95264000-95284000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr13:95264200-95299600	Weak transcription	Psoas Muscle	Psoas
13	chr13:95264600-95282400	Weak transcription	Pancreas	Pancrea
14	chr13:95264600-95289200	Weak transcription	Esophagus	oesophagus
15	chr13:95264600-95289600	Weak transcription	Fetal Kidney	kidney
16	chr13:95264800-95284600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr13:95265400-95286800	Weak transcription	A549	lung
18	chr13:95265600-95293400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr13:95268800-95283800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr13:95270000-95283400	Strong transcription	Dnd41	blood
21	chr13:95270400-95283400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr13:95270800-95283200	Strong transcription	Osteobl	bone
23	chr13:95271000-95283000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr13:95271000-95283600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr13:95271400-95282200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr13:95271600-95281800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr13:95272400-95282800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr13:95272600-95283400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr13:95274000-95284400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr13:95275200-95282600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr13:95275200-95284000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr13:95275400-95282400	Strong transcription	HMEC	breast
33	chr13:95275400-95283000	Strong transcription	NH-A	brain
34	chr13:95275400-95283200	Strong transcription	Fetal Thymus	thymus
35	chr13:95275400-95283400	Strong transcription	Adipose Nuclei	Adipose
36	chr13:95275800-95288800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr13:95276600-95292800	Weak transcription	Colon Smooth Muscle	Colon
38	chr13:95276600-95293600	Weak transcription	HSMMtube	muscle
39	chr13:95276800-95281400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr13:95276800-95284400	Weak transcription	Fetal Lung	lung
41	chr13:95276800-95284800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr13:95276800-95285000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr13:95276800-95286000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr13:95276800-95286200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr13:95276800-95287000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr13:95276800-95287400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr13:95276800-95288600	Weak transcription	Primary T cells from cord blood	blood
48	chr13:95276800-95288800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr13:95276800-95289000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr13:95276800-95292400	Weak transcription	NHEK	skin

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