Variant report

Variant	rs2941592
Chromosome Location	chr2:54846400-54846401
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54799047..54801001-chr2:54844688..54847061,2	MCF-7	breast:
2	chr2:54837203..54842761-chr2:54843020..54847377,6	K562	blood:
3	chr2:54843777..54846738-chr2:54866756..54869146,2	MCF-7	breast:
4	chr2:54844139..54846424-chr2:198364011..198365703,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144381	Chromatin interaction
ENSG00000115541	Chromatin interaction
ENSG00000270757	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1047465	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17046068	0.94[ASN][1000 genomes]
rs2229506	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2248749	0.92[CEU][hapmap]
rs28710338	0.87[ASN][1000 genomes]
rs2941581	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2941593	0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs2941594	0.80[AFR][1000 genomes]
rs2971878	0.88[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap];0.80[EUR][1000 genomes]
rs2971884	0.84[YRI][hapmap]
rs3769331	0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs3796013	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4426562	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60113783	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62134676	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62134679	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62134680	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62134681	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62134684	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62134700	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62134701	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62134705	0.80[AMR][1000 genomes]
rs62134706	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62134707	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62134708	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6724374	0.83[CEU][hapmap]
rs6748715	0.86[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs7583633	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs907136	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:137 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54829800-54859800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:54838800-54848800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:54838800-54860200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:54838800-54893400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:54839000-54846800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:54839000-54848200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:54839000-54864200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:54839200-54846800	Genic enhancers	Liver	Liver
9	chr2:54839200-54848600	Genic enhancers	Left Ventricle	heart
10	chr2:54839200-54861800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:54839200-54866000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:54839400-54853000	Strong transcription	Fetal Intestine Large	intestine
13	chr2:54839400-54895000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:54839600-54852400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:54839600-54862600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr2:54839800-54846800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr2:54839800-54847200	Genic enhancers	Fetal Lung	lung
18	chr2:54840800-54861400	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:54841000-54861400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:54841000-54861400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:54841200-54846800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:54841200-54847200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:54841200-54861200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:54841200-54897800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:54841600-54852400	Strong transcription	HSMMtube	muscle
26	chr2:54841600-54856200	Strong transcription	Hela-S3	cervix
27	chr2:54841600-54857000	Strong transcription	HSMM	muscle
28	chr2:54841800-54847000	Strong transcription	HMEC	breast
29	chr2:54841800-54857000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:54841800-54860000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:54841800-54860000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:54842000-54863600	Strong transcription	Fetal Brain Female	brain
33	chr2:54842400-54856800	Strong transcription	NH-A	brain
34	chr2:54842400-54861400	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:54842400-54862800	Strong transcription	NHEK	skin
36	chr2:54842600-54846800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:54842600-54861000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:54842600-54892000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:54842800-54846600	Genic enhancers	Rectal Smooth Muscle	rectum
40	chr2:54842800-54862400	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr2:54842800-54867800	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr2:54843000-54861400	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr2:54843400-54847200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:54844200-54847400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:54844200-54847400	Genic enhancers	Pancreas	Pancrea
46	chr2:54844200-54850000	Strong transcription	K562	blood
47	chr2:54844400-54847400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:54844400-54848600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr2:54844400-54860000	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr2:54844600-54846800	Genic enhancers	Primary T helper cells fromperipheralblood	blood

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