Variant report

Variant	rs9508554
Chromosome Location	chr13:30360860-30360861
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1058650	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11147398	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12872400	0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1323931	0.81[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1410110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1854176	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1927193	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2025604	0.83[ASN][1000 genomes]
rs2182129	0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2234416	0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2388246	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2388247	0.85[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2487664	0.82[AFR][1000 genomes]
rs2761938	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2761939	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2761940	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs278034	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2892463	0.85[YRI][hapmap]
rs35541102	0.88[ASN][1000 genomes]
rs4083610	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238128	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265673	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4297554	0.89[ASN][1000 genomes]
rs4769772	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4769775	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490429	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6490430	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72623487	0.81[ASN][1000 genomes]
rs7320474	0.89[ASN][1000 genomes]
rs7326253	0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7330356	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7335148	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7342470	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs765404	0.83[ASN][1000 genomes]
rs7981622	0.86[ASN][1000 genomes]
rs7995666	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9314972	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9314973	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9314974	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9314975	0.81[ASN][1000 genomes]
rs9314978	0.89[ASN][1000 genomes]
rs9506226	0.91[ASN][1000 genomes]
rs9506229	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9506231	0.81[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs9506233	0.85[ASN][1000 genomes]
rs9508550	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9508553	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs9508557	0.89[ASN][1000 genomes]
rs9508558	0.85[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs9508559	0.88[ASN][1000 genomes]
rs9508560	0.83[ASN][1000 genomes]
rs9508564	0.86[ASN][1000 genomes]
rs9508568	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9550494	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]
rs9551739	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9551741	0.82[ASN][1000 genomes]
rs9551744	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9551751	0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs9578136	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9578139	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[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:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30333200-30368200	Weak transcription	Aorta	Aorta
2	chr13:30333600-30376200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr13:30337600-30363000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:30339000-30364200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr13:30341200-30373200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr13:30341800-30363600	Weak transcription	HSMM	muscle
7	chr13:30341800-30365000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr13:30347600-30361800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr13:30347800-30361400	Weak transcription	A549	lung
10	chr13:30349800-30364400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr13:30350200-30361800	Weak transcription	Fetal Lung	lung
12	chr13:30350400-30361800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:30353400-30361600	Weak transcription	Brain Hippocampus Middle	brain
14	chr13:30354200-30361800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr13:30355400-30362000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr13:30357200-30363000	Weak transcription	Ovary	ovary
17	chr13:30357600-30364600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr13:30359000-30365600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr13:30359000-30367200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr13:30359800-30361000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr13:30359800-30361400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr13:30359800-30361400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr13:30359800-30362000	Enhancers	Duodenum Mucosa	Duodenum
24	chr13:30359800-30362600	Enhancers	Liver	Liver
25	chr13:30360000-30362400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr13:30360200-30361000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr13:30360200-30362800	Enhancers	Osteobl	bone
28	chr13:30360400-30362200	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr13:30360400-30362400	Weak transcription	Stomach Mucosa	stomach
30	chr13:30360400-30362600	Enhancers	Brain Substantia Nigra	brain
31	chr13:30360400-30363000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr13:30360400-30368000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr13:30360600-30361200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr13:30360600-30361600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr13:30360600-30361800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr13:30360600-30362000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr13:30360600-30362000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr13:30360600-30362000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr13:30360600-30362000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr13:30360600-30362000	Weak transcription	Small Intestine	intestine
41	chr13:30360600-30362600	Weak transcription	Gastric	stomach
42	chr13:30360600-30363000	Weak transcription	Left Ventricle	heart
43	chr13:30360600-30363000	Weak transcription	Pancreas	Pancrea
44	chr13:30360600-30363200	Weak transcription	Psoas Muscle	Psoas
45	chr13:30360600-30368000	Weak transcription	Fetal Intestine Large	intestine
46	chr13:30360600-30374800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr13:30360800-30361200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr13:30360800-30361200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr13:30360800-30361200	Weak transcription	NHDF-Ad	bronchial
50	chr13:30360800-30362400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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