Variant report

Variant	rs2439224
Chromosome Location	chr3:98611240-98611241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:98605105..98607853-chr3:98609864..98612381,4	K562	blood:
2	chr3:98610185..98614055-chr3:98618710..98621878,5	MCF-7	breast:
3	chr3:98601246..98603654-chr3:98609491..98611352,2	K562	blood:
4	chr3:98609933..98612061-chr3:98623742..98626335,2	K562	blood:

Variant related genes	Relation type
ENSG00000239462	Chromatin interaction
ENSG00000057019	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1062196	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs12054181	0.82[CHB][hapmap]
rs1440150	0.82[CHD][hapmap]
rs17270986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs1837500	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs1866677	0.81[CHB][hapmap]
rs1866678	0.82[CHB][hapmap]
rs1875086	0.81[ASN][1000 genomes]
rs2028393	0.81[ASN][1000 genomes]
rs2119187	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2119188	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs2246861	0.82[CHB][hapmap]
rs2247103	0.83[ASN][1000 genomes]
rs2439222	0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs2439223	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2439225	0.81[ASN][1000 genomes]
rs2439226	0.81[ASN][1000 genomes]
rs2439231	0.82[CHB][hapmap]
rs2439236	0.82[CHB][hapmap]
rs2454673	0.82[CHB][hapmap];0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs2454682	0.82[CHD][hapmap]
rs2454685	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2470825	0.82[CHB][hapmap]
rs2470852	0.84[ASN][1000 genomes]
rs2470857	0.82[CHB][hapmap]
rs2470859	0.82[CHB][hapmap]
rs2470861	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs2470867	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2470869	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2470881	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2470885	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs3755576	0.80[CHD][hapmap]
rs6782630	0.82[CHB][hapmap]
rs6785935	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs9289683	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs9811860	0.82[CHB][hapmap]
rs9814819	0.82[CHB][hapmap]
rs9823430	0.82[CHB][hapmap]
rs9835142	0.82[CHB][hapmap]
rs9843214	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs9852950	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs9873932	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98583400-98611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
3	chr3:98594400-98616600	Weak transcription	Fetal Brain Male	brain
4	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:98599800-98618400	Weak transcription	Fetal Brain Female	brain
6	chr3:98600600-98613000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:98600600-98618000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:98600600-98618000	Weak transcription	Fetal Thymus	thymus
9	chr3:98602200-98613600	Genic enhancers	HSMM	muscle
10	chr3:98602400-98613600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:98603200-98612600	Genic enhancers	NHEK	skin
12	chr3:98604000-98613000	Enhancers	NHLF	lung
13	chr3:98604200-98612600	Enhancers	NHDF-Ad	bronchial
14	chr3:98604400-98611400	Genic enhancers	HMEC	breast
15	chr3:98604400-98614600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:98604800-98612600	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:98605000-98618600	Weak transcription	Fetal Stomach	stomach
18	chr3:98605400-98611400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:98606400-98618400	Weak transcription	Fetal Kidney	kidney
20	chr3:98606600-98612600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:98606600-98618000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:98607600-98611800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:98607800-98612000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:98608000-98612400	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:98608800-98611800	Enhancers	HUVEC	blood vessel
26	chr3:98608800-98612000	Enhancers	Ovary	ovary
27	chr3:98608800-98614400	Enhancers	K562	blood
28	chr3:98609000-98612000	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr3:98609000-98612000	Enhancers	Stomach Smooth Muscle	stomach
30	chr3:98609000-98612600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:98609000-98612800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr3:98609000-98613200	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr3:98609000-98615800	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:98609200-98611400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr3:98609200-98611400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr3:98609200-98611600	Enhancers	Fetal Lung	lung
37	chr3:98609200-98613400	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr3:98609400-98612000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:98609400-98613400	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr3:98609400-98613800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:98609600-98613400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:98609800-98611800	Enhancers	Colon Smooth Muscle	Colon
43	chr3:98609800-98611800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr3:98609800-98612000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:98609800-98613800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:98609800-98614200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:98610000-98611800	Weak transcription	Aorta	Aorta
48	chr3:98610000-98612800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:98610200-98612600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr3:98610400-98611400	Enhancers	Skeletal Muscle Male	skeletal muscle

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