Variant report

Variant	rs1978997
Chromosome Location	chr10:49573590-49573591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:49559917..49561809-chr10:49572353..49575219,2	MCF-7	breast:
2	chr10:49571808..49574150-chr10:49719322..49721879,2	K562	blood:
3	chr10:49514674..49516304-chr10:49572941..49576035,3	K562	blood:
4	chr10:49571145..49574084-chr10:49715215..49717894,2	MCF-7	breast:
5	chr10:49514736..49516634-chr10:49571797..49574656,2	K562	blood:
6	chr10:49571896..49573651-chr10:49713045..49714727,3	K562	blood:
7	chr10:49571889..49574086-chr10:49706276..49707792,2	K562	blood:

Variant related genes	Relation type
ENSG00000248682	Chromatin interaction
ENSG00000107643	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10508902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10776601	1.00[CHB][hapmap]
rs11101311	1.00[ASN][1000 genomes]
rs12259267	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17010433	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17697960	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17697978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17698002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17698086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs17770456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17770535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17770554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17836191	0.85[CEU][hapmap]
rs35009243	1.00[ASN][1000 genomes]
rs3730156	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3730158	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs3730161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs4354648	1.00[ASN][1000 genomes]
rs4838403	0.85[CEU][hapmap]
rs57115982	1.00[ASN][1000 genomes]
rs57990560	1.00[ASN][1000 genomes]
rs61838674	1.00[ASN][1000 genomes]
rs61838676	1.00[ASN][1000 genomes]
rs61838695	1.00[ASN][1000 genomes]
rs61840551	1.00[ASN][1000 genomes]
rs61840552	1.00[ASN][1000 genomes]
rs61840553	1.00[ASN][1000 genomes]
rs61840555	0.90[ASN][1000 genomes]
rs724124	1.00[ASN][1000 genomes]
rs7478030	0.84[AMR][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	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 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	chr10:49543000-49576200	Weak transcription	Right Atrium	heart
2	chr10:49566400-49580000	Weak transcription	Colon Smooth Muscle	Colon
3	chr10:49568600-49582000	Weak transcription	Psoas Muscle	Psoas
4	chr10:49568800-49576400	Weak transcription	Ovary	ovary
5	chr10:49569400-49574400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr10:49571200-49573600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr10:49571200-49573600	Enhancers	Liver	Liver
8	chr10:49571200-49573600	Enhancers	K562	blood
9	chr10:49571200-49574600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr10:49571800-49573600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr10:49571800-49573600	Enhancers	Adipose Nuclei	Adipose
12	chr10:49571800-49573600	Enhancers	NH-A	brain
13	chr10:49571800-49573800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr10:49571800-49573800	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr10:49571800-49573800	Flanking Active TSS	A549	lung
16	chr10:49571800-49573800	Enhancers	HepG2	liver
17	chr10:49571800-49574000	Enhancers	Fetal Kidney	kidney
18	chr10:49571800-49574000	Enhancers	Osteobl	bone
19	chr10:49571800-49574200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr10:49571800-49574200	Flanking Active TSS	HUVEC	blood vessel
21	chr10:49571800-49574400	Enhancers	NHEK	skin
22	chr10:49571800-49574600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr10:49571800-49574600	Enhancers	Primary hematopoietic stem cells	blood
24	chr10:49571800-49574600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr10:49571800-49574600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr10:49571800-49574600	Enhancers	Fetal Lung	lung
27	chr10:49571800-49574600	Enhancers	NHDF-Ad	bronchial
28	chr10:49571800-49574600	Enhancers	NHLF	lung
29	chr10:49571800-49574800	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr10:49572000-49573600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr10:49572000-49574000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr10:49572000-49574000	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr10:49572000-49574400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr10:49572000-49574600	Enhancers	HMEC	breast
35	chr10:49572000-49577000	Weak transcription	Fetal Heart	heart
36	chr10:49572200-49574600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr10:49572200-49575800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr10:49572200-49585600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr10:49572600-49573600	Enhancers	Brain Substantia Nigra	brain
40	chr10:49572800-49573600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr10:49572800-49573800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr10:49572800-49574000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr10:49573000-49573600	Enhancers	Brain Anterior Caudate	brain
44	chr10:49573000-49574000	Enhancers	HSMM	muscle
45	chr10:49573000-49574400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr10:49573200-49573600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr10:49573200-49573600	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr10:49573200-49573600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr10:49573200-49573600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr10:49573200-49574000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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