Variant report

Variant	rs1234225
Chromosome Location	chr10:89673569-89673570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:89620299..89623441-chr10:89672450..89675807,5	MCF-7	breast:
2	chr10:89671146..89673722-chr10:89679466..89681540,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227268	Chromatin interaction
ENSG00000171862	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10430641	0.83[CHB][hapmap];0.93[CHD][hapmap]
rs10430642	0.82[CHB][hapmap]
rs11202615	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs1234212	0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1234213	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1234216	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1234224	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1236816	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1903858	0.88[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2248293	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2673803	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2735343	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs532678	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs555895	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1793518	chr10:89625582-89733420	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv1798260	chr10:89625582-89733420	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1035154	chr10:89657150-89676485	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3434490	chr10:89673470-89673933	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89633400-89675800	Weak transcription	Small Intestine	intestine
2	chr10:89647000-89711200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:89647200-89675400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr10:89648000-89683000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:89648200-89674400	Weak transcription	Right Ventricle	heart
6	chr10:89653200-89675200	Weak transcription	NHLF	lung
7	chr10:89656000-89675000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:89656600-89675800	Weak transcription	Osteobl	bone
9	chr10:89658400-89676400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr10:89663400-89675200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr10:89663400-89675200	Weak transcription	Gastric	stomach
12	chr10:89663600-89675200	Weak transcription	Pancreas	Pancrea
13	chr10:89663600-89686400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr10:89663600-89687400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr10:89663800-89675200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr10:89663800-89725400	Weak transcription	Colonic Mucosa	Colon
17	chr10:89664000-89674200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:89664000-89674800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr10:89664000-89675000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr10:89664000-89675200	Strong transcription	Fetal Thymus	thymus
21	chr10:89664000-89675200	Weak transcription	Left Ventricle	heart
22	chr10:89664000-89675200	Weak transcription	Lung	lung
23	chr10:89664000-89681800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr10:89664200-89674200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr10:89664200-89674400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr10:89664200-89675200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr10:89664600-89675200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr10:89664800-89675000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr10:89664800-89675000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr10:89664800-89675200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr10:89664800-89675200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr10:89664800-89676400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr10:89665200-89675200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr10:89665200-89675400	Weak transcription	NH-A	brain
35	chr10:89665600-89675200	Weak transcription	Esophagus	oesophagus
36	chr10:89666000-89712400	Weak transcription	Fetal Brain Male	brain
37	chr10:89666600-89675600	ZNF genes & repeats	GM12878-XiMat	blood
38	chr10:89666600-89682800	Weak transcription	Placenta	Placenta
39	chr10:89667000-89675400	Weak transcription	Fetal Heart	heart
40	chr10:89668000-89675200	Weak transcription	HMEC	breast
41	chr10:89668400-89675200	Weak transcription	Psoas Muscle	Psoas
42	chr10:89670000-89674000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr10:89670000-89674600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr10:89670200-89674600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
45	chr10:89670400-89674800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
46	chr10:89670400-89675000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr10:89670800-89674200	ZNF genes & repeats	Primary T cells from cord blood	blood
48	chr10:89671200-89674600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
49	chr10:89671400-89673600	ZNF genes & repeats	Adipose Nuclei	Adipose
50	chr10:89671400-89674000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood

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