Variant report

Variant	rs9568644
Chromosome Location	chr13:52198011-52198012
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52197836..52199878-chr13:52204458..52206730,2	MCF-7	breast:
2	chr13:52023768..52028038-chr13:52196089..52202067,6	MCF-7	breast:
3	chr13:52196868..52198999-chr13:52337488..52339399,2	K562	blood:

Variant related genes	Relation type
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1024271	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes]
rs12585249	0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes]
rs17075902	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3803201	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3825410	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4075628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4625625	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4941703	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4941710	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4943005	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4943009	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[EUR][1000 genomes]
rs4943018	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7328589	0.82[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes]
rs7328695	0.81[AMR][1000 genomes]
rs7333623	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs745374	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7986066	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9316547	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs9316548	0.86[ASN][1000 genomes]
rs9316551	0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9563063	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9563065	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9563066	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9563067	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9568633	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9568647	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9568649	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9568650	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9568653	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9568658	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9805172	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52188800-52199200	Weak transcription	Liver	Liver
2	chr13:52189400-52205600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr13:52189400-52206600	Weak transcription	Primary B cells from cord blood	blood
4	chr13:52189400-52208800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr13:52190400-52205000	Enhancers	NHDF-Ad	bronchial
6	chr13:52191400-52201400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr13:52191600-52201200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr13:52192200-52204800	Enhancers	Brain Substantia Nigra	brain
9	chr13:52192400-52204000	Enhancers	HSMMtube	muscle
10	chr13:52192800-52205600	Weak transcription	A549	lung
11	chr13:52193200-52199600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr13:52193600-52201800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr13:52194000-52199600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr13:52194200-52198400	Weak transcription	NHEK	skin
15	chr13:52194200-52202200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr13:52194200-52209400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr13:52194600-52201200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr13:52194800-52198600	Weak transcription	Psoas Muscle	Psoas
19	chr13:52194800-52199200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr13:52194800-52199200	Weak transcription	Colon Smooth Muscle	Colon
21	chr13:52194800-52202200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr13:52194800-52205600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr13:52194800-52217600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr13:52195000-52198800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr13:52195000-52198800	Weak transcription	Gastric	stomach
26	chr13:52195000-52199000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr13:52195000-52199600	Enhancers	HSMM	muscle
28	chr13:52195000-52199800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr13:52195000-52200800	Weak transcription	Right Ventricle	heart
30	chr13:52195000-52201000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr13:52195000-52201000	Weak transcription	Esophagus	oesophagus
32	chr13:52195000-52202200	Weak transcription	Spleen	Spleen
33	chr13:52195000-52202400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr13:52195000-52205600	Enhancers	Muscle Satellite Cultured Cells	--
35	chr13:52195200-52198200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr13:52195200-52198400	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr13:52195200-52198600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr13:52195200-52199000	Weak transcription	Aorta	Aorta
39	chr13:52195200-52199800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr13:52195200-52199800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr13:52195200-52200200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr13:52195200-52201000	Enhancers	Brain Hippocampus Middle	brain
43	chr13:52195400-52198400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr13:52195400-52199200	Weak transcription	Adipose Nuclei	Adipose
45	chr13:52195400-52201400	Enhancers	HepG2	liver
46	chr13:52195600-52198800	Weak transcription	Left Ventricle	heart
47	chr13:52195600-52198800	Weak transcription	Right Atrium	heart
48	chr13:52195600-52199200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr13:52196000-52198800	Weak transcription	Pancreas	Pancrea
50	chr13:52196000-52207200	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links