Variant report

Variant	rs11596959
Chromosome Location	chr10:5740688-5740689
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr10:5739315-5740745	PBDE	blood:	n/a	chr10:5739624-5739645 chr10:5739631-5739638
2	RUNX3	chr10:5740292-5740693	GM12878	blood:	n/a	chr10:5740426-5740435 chr10:5740426-5740435

No.	Distal block	Cell Line	Cell type
1	chr10:5706900..5709374-chr10:5740250..5741979,2	MCF-7	breast:
2	chr10:5724274..5728540-chr10:5734829..5741563,8	MCF-7	breast:
3	chr10:5729840..5732495-chr10:5739235..5741106,2	MCF-7	breast:
4	chr10:5726410..5728417-chr10:5738015..5741917,3	MCF-7	breast:
5	chr10:5734758..5736346-chr10:5739333..5741720,2	MCF-7	breast:
6	chr10:5733360..5736300-chr10:5737628..5741126,5	MCF-7	breast:
7	chr10:5739796..5741781-chr10:5749171..5751664,2	K562	blood:

Variant related genes	Relation type
FAM208B	TF binding region
ENSG00000108021	Chromatin interaction
ENSG00000196372	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11254898	0.87[ASW][hapmap]
rs11592184	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11592260	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11592964	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11593253	0.85[ASN][1000 genomes]
rs11593616	0.90[ASN][1000 genomes]
rs11594216	1.00[JPT][hapmap]
rs11595445	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11595457	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11595970	0.85[ASN][1000 genomes]
rs11596603	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11596815	0.90[ASN][1000 genomes]
rs11597597	0.85[ASN][1000 genomes]
rs11598956	1.00[JPT][hapmap]
rs1418739	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1512695	0.87[ASW][hapmap];0.92[LWK][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap]
rs17142551	1.00[JPT][hapmap]
rs17143106	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs2797485	0.83[AFR][1000 genomes]
rs2797498	0.89[YRI][hapmap]
rs2892072	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4237385	0.89[YRI][hapmap]
rs45584541	0.88[EUR][1000 genomes]
rs59511159	0.90[ASN][1000 genomes]
rs60255716	0.90[ASN][1000 genomes]
rs60467900	0.89[AFR][1000 genomes]
rs61611877	1.00[ASN][1000 genomes]
rs73610563	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73610574	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73610587	0.89[AFR][1000 genomes]
rs73610592	0.89[AFR][1000 genomes]
rs73610598	0.83[AFR][1000 genomes]
rs9423934	1.00[GIH][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	esv1796213	chr10:5716555-5766165	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv522415	chr10:5721653-5768493	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv1050663	chr10:5737979-5785918	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv528504	chr10:5739054-5754611	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5728800-5746800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr10:5734800-5763400	Weak transcription	HSMM	muscle
3	chr10:5735200-5743000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr10:5735200-5749000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr10:5735200-5750600	Weak transcription	Gastric	stomach
6	chr10:5735200-5767000	Weak transcription	Fetal Muscle Leg	muscle
7	chr10:5735400-5744800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr10:5735400-5750800	Weak transcription	Spleen	Spleen
9	chr10:5735400-5761600	Weak transcription	NHEK	skin
10	chr10:5735400-5762000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr10:5735800-5741800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr10:5735800-5752800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr10:5736200-5742600	Weak transcription	Brain Angular Gyrus	brain
14	chr10:5736200-5751600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr10:5736400-5741000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr10:5736400-5753000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:5736600-5741600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr10:5736800-5742000	Weak transcription	Primary T cells from cord blood	blood
19	chr10:5736800-5742000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr10:5737000-5742000	Weak transcription	Brain Substantia Nigra	brain
21	chr10:5737000-5742600	Weak transcription	Brain Hippocampus Middle	brain
22	chr10:5737000-5743600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr10:5737400-5744200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr10:5737400-5744800	Weak transcription	Liver	Liver
25	chr10:5737600-5740800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr10:5737600-5744200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr10:5738200-5745200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr10:5738400-5741000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr10:5738400-5741400	Enhancers	K562	blood
30	chr10:5738400-5744200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr10:5738600-5740800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr10:5738600-5752400	Weak transcription	Primary B cells from cord blood	blood
33	chr10:5738600-5752800	Weak transcription	Right Atrium	heart
34	chr10:5738600-5769000	Weak transcription	Left Ventricle	heart
35	chr10:5739200-5741000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr10:5739400-5741400	Enhancers	Small Intestine	intestine
37	chr10:5739400-5741600	Enhancers	Primary B cells from peripheral blood	blood
38	chr10:5739400-5745000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr10:5739600-5740800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr10:5739600-5752800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr10:5739800-5741200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr10:5740200-5741200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr10:5740200-5741400	Strong transcription	A549	lung
44	chr10:5740200-5742000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr10:5740200-5742400	Weak transcription	HepG2	liver
46	chr10:5740200-5752000	Weak transcription	Stomach Mucosa	stomach
47	chr10:5740200-5752800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr10:5740400-5740800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr10:5740400-5740800	Weak transcription	GM12878-XiMat	blood
50	chr10:5740400-5742200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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