Variant report

Variant	rs9550494
Chromosome Location	chr13:30376259-30376260
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1058650	0.89[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs11147398	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12872400	0.81[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1323931	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1410110	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1772727	0.82[AFR][1000 genomes]
rs1854176	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1886170	0.91[YRI][hapmap]
rs1927193	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2025604	0.83[ASN][1000 genomes]
rs2182129	0.85[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs2234416	0.89[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2388244	0.87[YRI][hapmap]
rs2388246	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2388247	0.89[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs2761938	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2761939	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2761940	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278034	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278037	0.91[YRI][hapmap]
rs35541102	0.88[ASN][1000 genomes]
rs4083610	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4238128	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4265673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4297554	0.89[ASN][1000 genomes]
rs4769772	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4769774	0.91[YRI][hapmap]
rs4769775	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6490429	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6490430	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7320474	0.89[ASN][1000 genomes]
rs7326253	0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7330356	0.94[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7335148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7342470	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs765404	0.83[ASN][1000 genomes]
rs7981622	0.86[ASN][1000 genomes]
rs7995666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9314972	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9314973	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9314974	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9314978	0.89[ASN][1000 genomes]
rs9506226	0.88[ASN][1000 genomes]
rs9506229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9506230	0.85[AFR][1000 genomes]
rs9506231	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs9506233	0.85[ASN][1000 genomes]
rs9508550	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9508553	0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs9508554	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9508555	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs9508557	0.89[ASN][1000 genomes]
rs9508558	0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs9508559	0.88[ASN][1000 genomes]
rs9508560	0.84[ASN][1000 genomes]
rs9508564	0.86[ASN][1000 genomes]
rs9508568	0.92[ASN][1000 genomes]
rs9551739	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9551744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9551751	0.89[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs9578136	0.85[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9578139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30363800-30385000	Weak transcription	Left Ventricle	heart
2	chr13:30365800-30383200	Weak transcription	Ovary	ovary
3	chr13:30366200-30381400	Weak transcription	Stomach Mucosa	stomach
4	chr13:30372800-30378000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr13:30372800-30378000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr13:30373000-30377800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr13:30373200-30376600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr13:30373200-30377600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr13:30373400-30383200	Weak transcription	Small Intestine	intestine
10	chr13:30374000-30380200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr13:30374200-30376400	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr13:30374200-30377000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr13:30374200-30380800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr13:30374200-30383200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr13:30374400-30376600	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr13:30374400-30377200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr13:30374800-30376400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:30374800-30376600	Enhancers	H9 Cell Line	embryonic stem cell
19	chr13:30374800-30376600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr13:30374800-30376600	Enhancers	Placenta Amnion	Placenta Amnion
21	chr13:30375000-30376400	Enhancers	Spleen	Spleen
22	chr13:30375000-30376600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr13:30375000-30376600	Enhancers	Psoas Muscle	Psoas
24	chr13:30375200-30376400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr13:30375200-30376400	Enhancers	Primary T cells fromperipheralblood	blood
26	chr13:30375200-30376400	Enhancers	Gastric	stomach
27	chr13:30375200-30376400	Enhancers	Pancreas	Pancrea
28	chr13:30375200-30376600	Enhancers	Brain Substantia Nigra	brain
29	chr13:30375200-30376800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:30375200-30377200	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr13:30375200-30377400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr13:30375200-30377600	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr13:30375400-30376400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr13:30375400-30376400	Enhancers	Brain Anterior Caudate	brain
35	chr13:30375400-30376600	Enhancers	Lung	lung
36	chr13:30375400-30376800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr13:30375400-30383200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr13:30375600-30376400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr13:30375600-30376600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr13:30375600-30376600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr13:30375600-30376600	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr13:30375600-30377200	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr13:30375600-30377200	Enhancers	Adipose Nuclei	Adipose
44	chr13:30375600-30377600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr13:30375800-30376400	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr13:30375800-30376400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr13:30375800-30376600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr13:30375800-30376600	Enhancers	Primary B cells from peripheral blood	blood
49	chr13:30375800-30376600	Enhancers	GM12878-XiMat	blood
50	chr13:30375800-30376800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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