Variant report

Variant	rs9508553
Chromosome Location	chr13:30357155-30357156
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30355832..30358198-chr13:30363534..30365177,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1058650	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11147398	0.89[ASN][1000 genomes]
rs12872400	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1323931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1410110	0.85[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2025604	0.90[ASN][1000 genomes]
rs2182129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2234416	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2388246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2388247	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2761938	0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2761939	0.84[ASN][1000 genomes]
rs2761940	0.81[ASN][1000 genomes]
rs278034	0.81[ASN][1000 genomes]
rs278049	0.82[CHB][hapmap]
rs35541102	0.95[ASN][1000 genomes]
rs3818368	0.82[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.80[EUR][1000 genomes]
rs4083610	0.83[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs4238128	0.91[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs4265673	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4297554	0.96[ASN][1000 genomes]
rs4769775	0.89[ASN][1000 genomes]
rs6490429	0.87[ASN][1000 genomes]
rs6490430	0.87[ASN][1000 genomes]
rs72623487	0.88[ASN][1000 genomes]
rs7320474	0.96[ASN][1000 genomes]
rs7326253	0.81[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs7330356	0.82[CHB][hapmap]
rs7335148	0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs765404	0.90[ASN][1000 genomes]
rs7981622	0.93[ASN][1000 genomes]
rs7995666	0.91[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs9314975	0.88[ASN][1000 genomes]
rs9314978	0.96[ASN][1000 genomes]
rs9506226	0.98[ASN][1000 genomes]
rs9506229	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9506231	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9506233	0.92[ASN][1000 genomes]
rs9508554	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs9508557	0.96[ASN][1000 genomes]
rs9508558	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9508559	0.95[ASN][1000 genomes]
rs9508560	0.90[ASN][1000 genomes]
rs9508561	0.85[ASN][1000 genomes]
rs9508564	0.93[ASN][1000 genomes]
rs9508568	0.81[ASN][1000 genomes]
rs9508575	0.82[CEU][hapmap]
rs9550494	0.89[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs9551741	0.89[ASN][1000 genomes]
rs9551744	0.91[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs9551751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9551753	0.90[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs9551755	0.88[EUR][1000 genomes]
rs9578136	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9578139	0.91[CHB][hapmap];0.85[JPT][hapmap];0.87[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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30333200-30360200	Weak transcription	Pancreas	Pancrea
2	chr13:30333200-30368200	Weak transcription	Aorta	Aorta
3	chr13:30333600-30376200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr13:30337600-30363000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:30337800-30359800	Weak transcription	HMEC	breast
6	chr13:30338400-30360000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr13:30338400-30360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr13:30339000-30360200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr13:30339000-30364200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr13:30341200-30373200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr13:30341400-30360200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr13:30341600-30357200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr13:30341600-30360200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr13:30341800-30359800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr13:30341800-30360200	Weak transcription	Left Ventricle	heart
16	chr13:30341800-30360400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr13:30341800-30363600	Weak transcription	HSMM	muscle
18	chr13:30341800-30365000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr13:30342000-30359800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr13:30343800-30360200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr13:30344400-30359600	Weak transcription	Primary T cells from cord blood	blood
22	chr13:30344400-30360200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr13:30345800-30360200	Weak transcription	Small Intestine	intestine
24	chr13:30346600-30359800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr13:30347600-30361800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr13:30347800-30361400	Weak transcription	A549	lung
27	chr13:30349200-30360200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr13:30349800-30364400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr13:30350000-30360000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr13:30350200-30357600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr13:30350200-30358200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr13:30350200-30361800	Weak transcription	Fetal Lung	lung
33	chr13:30350400-30359800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr13:30350400-30361800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr13:30350800-30359800	Weak transcription	Fetal Intestine Small	intestine
36	chr13:30351200-30360200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr13:30353400-30361600	Weak transcription	Brain Hippocampus Middle	brain
38	chr13:30354200-30360200	Weak transcription	Gastric	stomach
39	chr13:30354200-30361800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr13:30355400-30362000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr13:30356600-30357600	Enhancers	Liver	Liver
42	chr13:30356600-30359600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr13:30356800-30357200	Flanking Active TSS	GM12878-XiMat	blood
44	chr13:30356800-30357600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr13:30356800-30357600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr13:30356800-30358000	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr13:30357000-30357200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr13:30357000-30357200	Enhancers	Brain Angular Gyrus	brain
49	chr13:30357000-30357200	Enhancers	Ovary	ovary
50	chr13:30357000-30357200	Genic enhancers	NHDF-Ad	bronchial

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