Variant report

Variant	rs9535720
Chromosome Location	chr13:52194944-52194945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52024726..52028383-chr13:52193377..52195964,3	K562	blood:
2	chr13:52194627..52196438-chr13:52199246..52202202,2	K562	blood:

Variant related genes	Relation type
ENSG00000102786	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000224892	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1885855	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1923874	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4456399	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.83[ASN][1000 genomes]
rs4533167	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4943008	0.84[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4943014	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6561644	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7320201	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7327107	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7984225	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7988297	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7990679	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9285179	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526792	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535716	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs992583	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[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	chr13:52188800-52195800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr13:52188800-52197000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr13:52188800-52199200	Weak transcription	Liver	Liver
4	chr13:52189000-52197400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr13:52189000-52197800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr13:52189200-52195800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr13:52189200-52196200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr13:52189200-52196200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr13:52189200-52197200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr13:52189400-52197200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr13:52189400-52197200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr13:52189400-52205600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr13:52189400-52206600	Weak transcription	Primary B cells from cord blood	blood
14	chr13:52189400-52208800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr13:52190400-52196200	Enhancers	Fetal Heart	heart
16	chr13:52190400-52205000	Enhancers	NHDF-Ad	bronchial
17	chr13:52190600-52196800	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr13:52191400-52195200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr13:52191400-52201400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr13:52191600-52195000	Enhancers	Osteobl	bone
21	chr13:52191600-52195200	Enhancers	Ovary	ovary
22	chr13:52191600-52196400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr13:52191600-52197600	Enhancers	Brain Cingulate Gyrus	brain
24	chr13:52191600-52201200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr13:52192200-52195400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr13:52192200-52196600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:52192200-52196800	Enhancers	Brain Anterior Caudate	brain
28	chr13:52192200-52196800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr13:52192200-52204800	Enhancers	Brain Substantia Nigra	brain
30	chr13:52192400-52195200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:52192400-52195400	Enhancers	NHLF	lung
32	chr13:52192400-52204000	Enhancers	HSMMtube	muscle
33	chr13:52192600-52195000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr13:52192800-52195000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr13:52192800-52195200	Enhancers	NH-A	brain
36	chr13:52192800-52195600	Enhancers	Right Atrium	heart
37	chr13:52192800-52195800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr13:52192800-52196400	Enhancers	Fetal Muscle Leg	muscle
39	chr13:52192800-52205600	Weak transcription	A549	lung
40	chr13:52193000-52195000	Enhancers	HepG2	liver
41	chr13:52193000-52195800	Weak transcription	Brain Germinal Matrix	brain
42	chr13:52193200-52195800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr13:52193200-52196200	Weak transcription	Fetal Brain Female	brain
44	chr13:52193200-52197200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr13:52193200-52199600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr13:52193400-52195400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr13:52193400-52196600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr13:52193600-52196800	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr13:52193600-52201800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr13:52193800-52195000	Flanking Active TSS	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links