Variant report

Variant	rs60199254
Chromosome Location	chr2:46778268-46778269
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	chr2:46776310..46779098-chr2:46785814..46787869,2	MCF-7	breast:
2	chr2:46769168..46772138-chr2:46777700..46782112,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119729	Chromatin interaction
ENSG00000250565	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11903907	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13404342	0.86[EUR][1000 genomes]
rs1456010	0.82[ASN][1000 genomes]
rs17035272	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1809087	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59823825	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6735530	0.87[ASN][1000 genomes]
rs6749372	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72875696	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7591561	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs962467	0.93[EUR][1000 genomes]
rs9808496	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS 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	35 gene(s)	inside rSNPs	diseases
8	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv9713	chr2:46775356-46790566	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46771000-46781600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:46771200-46780000	Enhancers	Psoas Muscle	Psoas
3	chr2:46771200-46781400	Weak transcription	NHEK	skin
4	chr2:46771200-46781600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:46771200-46781600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:46771200-46812800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:46771400-46780000	Genic enhancers	Fetal Muscle Leg	muscle
8	chr2:46771400-46781600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:46771400-46789600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:46771400-46796000	Weak transcription	Fetal Kidney	kidney
11	chr2:46771600-46781600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:46771600-46781600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:46771800-46780000	Enhancers	Right Atrium	heart
14	chr2:46771800-46781400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:46771800-46781400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:46771800-46781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:46771800-46782000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:46771800-46782400	Weak transcription	HMEC	breast
19	chr2:46771800-46795600	Weak transcription	Fetal Brain Male	brain
20	chr2:46772000-46782600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:46772200-46780200	Genic enhancers	Left Ventricle	heart
22	chr2:46772200-46804000	Weak transcription	NH-A	brain
23	chr2:46773000-46780200	Strong transcription	Osteobl	bone
24	chr2:46773200-46806000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:46773400-46779800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:46773600-46778600	Genic enhancers	Brain Hippocampus Middle	brain
27	chr2:46774000-46779800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr2:46774400-46778400	Enhancers	Thymus	Thymus
29	chr2:46774400-46782200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:46774600-46778600	Enhancers	Primary T cells fromperipheralblood	blood
31	chr2:46774600-46778800	Genic enhancers	Right Ventricle	heart
32	chr2:46774600-46780000	Genic enhancers	Spleen	Spleen
33	chr2:46774800-46781400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:46774800-46789200	Weak transcription	Pancreas	Pancrea
35	chr2:46775200-46778600	Weak transcription	HepG2	liver
36	chr2:46775200-46782400	Weak transcription	Fetal Lung	lung
37	chr2:46775200-46787200	Weak transcription	Gastric	stomach
38	chr2:46775200-46788600	Weak transcription	A549	lung
39	chr2:46775400-46778600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:46775400-46778600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:46775400-46779400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:46775400-46782600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:46775600-46778600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:46775600-46815800	Weak transcription	Fetal Brain Female	brain
45	chr2:46775800-46778400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:46775800-46779600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:46775800-46780200	Genic enhancers	Fetal Muscle Trunk	muscle
48	chr2:46776000-46778400	Genic enhancers	Primary hematopoietic stem cells	blood
49	chr2:46776000-46781400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr2:46776400-46779400	Weak transcription	Fetal Intestine Small	intestine

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