Variant report

Variant	rs1234224
Chromosome Location	chr10:89675296-89675297
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	chr10:89620299..89623441-chr10:89672450..89675807,5	MCF-7	breast:
2	chr10:89673644..89678140-chr10:89679296..89683460,5	K562	blood:

Variant related genes	Relation type
ENSG00000227268	Chromatin interaction
ENSG00000171862	Chromatin interaction

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

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

rs_ID	r²[population]
rs10430641	0.87[CHB][hapmap]
rs10430642	0.87[CHB][hapmap]
rs11202615	0.87[CHB][hapmap]
rs1234212	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1234213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1234216	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1234225	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	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1903858	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2248293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2673803	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2735343	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs532678	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs555895	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:117 , 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	chr10:89656600-89675800	Weak transcription	Osteobl	bone
6	chr10:89658400-89676400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr10:89663600-89686400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr10:89663600-89687400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:89663800-89725400	Weak transcription	Colonic Mucosa	Colon
10	chr10:89664000-89681800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr10:89664800-89676400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr10:89665200-89675400	Weak transcription	NH-A	brain
13	chr10:89666000-89712400	Weak transcription	Fetal Brain Male	brain
14	chr10:89666600-89675600	ZNF genes & repeats	GM12878-XiMat	blood
15	chr10:89666600-89682800	Weak transcription	Placenta	Placenta
16	chr10:89667000-89675400	Weak transcription	Fetal Heart	heart
17	chr10:89671600-89675400	ZNF genes & repeats	Fetal Intestine Large	intestine
18	chr10:89671600-89675400	ZNF genes & repeats	Fetal Muscle Leg	muscle
19	chr10:89671600-89675600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
20	chr10:89671600-89682800	Weak transcription	Spleen	Spleen
21	chr10:89672000-89681600	Weak transcription	Aorta	Aorta
22	chr10:89673200-89675600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr10:89673400-89679800	Genic enhancers	Dnd41	blood
24	chr10:89673600-89675400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr10:89673600-89675400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:89673600-89676200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr10:89673600-89679400	Weak transcription	Brain Hippocampus Middle	brain
28	chr10:89673600-89726000	Weak transcription	Brain Substantia Nigra	brain
29	chr10:89673800-89676000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr10:89674000-89685600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr10:89674200-89675400	Weak transcription	Primary T cells from cord blood	blood
32	chr10:89674200-89675600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
33	chr10:89674200-89675600	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr10:89674200-89676400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr10:89674200-89695200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr10:89674200-89711000	Weak transcription	HepG2	liver
37	chr10:89674400-89675400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr10:89674400-89675400	Strong transcription	Ovary	ovary
39	chr10:89674400-89675600	ZNF genes & repeats	Fetal Stomach	stomach
40	chr10:89674400-89675600	Enhancers	HUVEC	blood vessel
41	chr10:89674600-89675800	Strong transcription	Primary B cells from cord blood	blood
42	chr10:89674600-89675800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr10:89674600-89678400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr10:89674600-89682600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr10:89674600-89684400	Weak transcription	Fetal Kidney	kidney
46	chr10:89674600-89686400	Weak transcription	HSMMtube	muscle
47	chr10:89674600-89687000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr10:89674600-89689800	Weak transcription	Fetal Lung	lung
49	chr10:89674600-89695600	Weak transcription	Fetal Muscle Trunk	muscle
50	chr10:89674800-89678800	Enhancers	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links