Variant report

Variant	rs2226078
Chromosome Location	chr13:95284231-95284232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs16949940	0.80[CEU][hapmap]
rs16949977	1.00[ASN][1000 genomes]
rs2146822	1.00[ASN][1000 genomes]
rs2226077	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417425	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4516070	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59149020	1.00[ASN][1000 genomes]
rs61707735	1.00[ASN][1000 genomes]
rs61965606	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492722	1.00[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492724	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72638354	1.00[ASN][1000 genomes]
rs72638356	1.00[ASN][1000 genomes]
rs7318105	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320230	1.00[ASN][1000 genomes]
rs7329965	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329985	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73546690	1.00[ASN][1000 genomes]
rs7981150	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984105	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7989918	1.00[ASN][1000 genomes]
rs7998457	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516431	1.00[ASN][1000 genomes]
rs9516436	0.80[CEU][hapmap];1.00[CHD][hapmap]
rs9516439	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524564	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524575	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9524577	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9584241	1.00[ASN][1000 genomes]
rs9584242	1.00[ASN][1000 genomes]
rs9584243	1.00[ASN][1000 genomes]
rs9590039	0.80[CEU][hapmap];1.00[CHD][hapmap]
rs9590043	0.80[CEU][hapmap]
rs9590045	1.00[ASN][1000 genomes]
rs9590046	1.00[ASN][1000 genomes]
rs9590048	1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2226078	GPR180	cis	Muscle Skeletal	GTEx
rs2226078	GPR180	cis	parietal	SCAN
rs2226078	GPR180	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95254800-95288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:95255400-95288600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr13:95255800-95285000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr13:95260000-95285800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr13:95264200-95299600	Weak transcription	Psoas Muscle	Psoas
6	chr13:95264600-95289200	Weak transcription	Esophagus	oesophagus
7	chr13:95264600-95289600	Weak transcription	Fetal Kidney	kidney
8	chr13:95264800-95284600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr13:95265400-95286800	Weak transcription	A549	lung
10	chr13:95265600-95293400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:95274000-95284400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr13:95275800-95288800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr13:95276600-95292800	Weak transcription	Colon Smooth Muscle	Colon
14	chr13:95276600-95293600	Weak transcription	HSMMtube	muscle
15	chr13:95276800-95284400	Weak transcription	Fetal Lung	lung
16	chr13:95276800-95284800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr13:95276800-95285000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:95276800-95286000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr13:95276800-95286200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr13:95276800-95287000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr13:95276800-95287400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr13:95276800-95288600	Weak transcription	Primary T cells from cord blood	blood
23	chr13:95276800-95288800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr13:95276800-95289000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr13:95276800-95292400	Weak transcription	NHEK	skin
26	chr13:95276800-95292800	Weak transcription	NHLF	lung
27	chr13:95276800-95294000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr13:95277000-95286200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr13:95277000-95289200	Weak transcription	Brain Hippocampus Middle	brain
30	chr13:95277200-95285200	Weak transcription	Thymus	Thymus
31	chr13:95277200-95287600	Weak transcription	Fetal Brain Female	brain
32	chr13:95277200-95291200	Weak transcription	Primary B cells from cord blood	blood
33	chr13:95277200-95293000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr13:95277400-95285000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr13:95277400-95285600	Weak transcription	Fetal Intestine Small	intestine
36	chr13:95277400-95287600	Weak transcription	Fetal Stomach	stomach
37	chr13:95277400-95289800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr13:95277400-95293400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr13:95277400-95293800	Weak transcription	Ovary	ovary
40	chr13:95277800-95293200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr13:95278200-95284800	Weak transcription	Placenta	Placenta
42	chr13:95278800-95289200	Weak transcription	Fetal Intestine Large	intestine
43	chr13:95279400-95287600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr13:95279600-95289200	Weak transcription	Brain Anterior Caudate	brain
45	chr13:95279800-95289000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr13:95280200-95284600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr13:95280200-95284800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr13:95280400-95284400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr13:95280600-95286000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr13:95280600-95293000	Weak transcription	HUVEC	blood vessel

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