Variant report

Variant	rs2060561
Chromosome Location	chr10:52103126-52103127
allele	A/T
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	POLR2A	chr10:52082643-52104294	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:52100945..52103388-chr10:52103997..52106988,2	MCF-7	breast:

Variant related genes	Relation type
SGMS1	TF binding region
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11005215	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11005290	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1344848	0.93[CEU][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes]
rs1436212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1436214	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17785945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60381888	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7911266	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518071	chr10:51595893-52157935	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1053903	chr10:51886486-52163991	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1040661	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1051028	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1037118	chr10:51886486-52167442	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	esv2830205	chr10:51978430-52135215	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv1046850	chr10:52009869-52135542	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv540625	chr10:52009869-52135542	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
14	esv2762864	chr10:52030945-52107415	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
15	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52071200-52103200	Weak transcription	Thymus	Thymus
2	chr10:52071200-52103400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:52071200-52103400	Weak transcription	Esophagus	oesophagus
4	chr10:52076400-52103200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:52084000-52103200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr10:52084400-52103400	Weak transcription	Spleen	Spleen
7	chr10:52085800-52103400	Weak transcription	Pancreas	Pancrea
8	chr10:52087000-52103200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr10:52087000-52103400	Weak transcription	Aorta	Aorta
10	chr10:52087000-52105800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr10:52087000-52106800	Weak transcription	Brain Angular Gyrus	brain
12	chr10:52087200-52103200	Weak transcription	Fetal Stomach	stomach
13	chr10:52087200-52107400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr10:52087400-52103200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:52087400-52103200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr10:52087400-52103200	Weak transcription	Brain Anterior Caudate	brain
17	chr10:52087400-52104800	Weak transcription	NH-A	brain
18	chr10:52087600-52106600	Weak transcription	Psoas Muscle	Psoas
19	chr10:52087600-52106600	Weak transcription	Stomach Mucosa	stomach
20	chr10:52087800-52107400	Weak transcription	NHEK	skin
21	chr10:52090800-52106800	Weak transcription	NHDF-Ad	bronchial
22	chr10:52092200-52103200	Weak transcription	Fetal Intestine Small	intestine
23	chr10:52092200-52103400	Weak transcription	Ovary	ovary
24	chr10:52092200-52104200	Weak transcription	Fetal Heart	heart
25	chr10:52093800-52105000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr10:52094000-52103400	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr10:52094600-52109000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr10:52094800-52105600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:52095000-52109000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr10:52095200-52107200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr10:52095200-52119000	Weak transcription	Fetal Kidney	kidney
32	chr10:52095400-52103200	Weak transcription	Left Ventricle	heart
33	chr10:52095400-52106200	Weak transcription	HSMMtube	muscle
34	chr10:52095400-52118200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr10:52096400-52123000	Weak transcription	Small Intestine	intestine
36	chr10:52097200-52103400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr10:52097600-52107000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr10:52098800-52103400	Strong transcription	GM12878-XiMat	blood
39	chr10:52098800-52104200	Strong transcription	Primary T cells from cord blood	blood
40	chr10:52099000-52103400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr10:52099000-52104200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr10:52099200-52103400	Weak transcription	Gastric	stomach
43	chr10:52099600-52103400	Weak transcription	Colonic Mucosa	Colon
44	chr10:52099600-52104200	Strong transcription	Liver	Liver
45	chr10:52100000-52103400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr10:52100200-52103400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr10:52100400-52103200	Weak transcription	Fetal Thymus	thymus
48	chr10:52100600-52103200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr10:52100800-52104000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr10:52100800-52104200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links