Variant report

Variant	rs41281495
Chromosome Location	chr2:54845490-54845491
allele	A/C
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
ENSG00000270757	Chromatin interaction
ENSG00000115541	Chromatin interaction
ENSG00000144381	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13405115	0.85[EUR][1000 genomes]
rs17343918	0.83[EUR][1000 genomes]
rs17344134	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17344169	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17344176	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17344287	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17344308	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17344343	1.00[EUR][1000 genomes]
rs17415829	0.83[EUR][1000 genomes]
rs17415857	0.83[EUR][1000 genomes]
rs17416130	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17416291	1.00[EUR][1000 genomes]
rs17416820	0.87[EUR][1000 genomes]
rs17521468	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17521510	1.00[EUR][1000 genomes]
rs17580855	1.00[EUR][1000 genomes]
rs17580876	1.00[EUR][1000 genomes]
rs1804472	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796015	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41281497	1.00[EUR][1000 genomes]
rs4258834	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4440005	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57810131	0.80[EUR][1000 genomes]
rs58143357	0.80[EUR][1000 genomes]
rs58987524	0.81[AFR][1000 genomes]
rs59228485	0.91[EUR][1000 genomes]
rs61480394	0.91[EUR][1000 genomes]
rs6755737	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911560	0.83[EUR][1000 genomes]
rs72911563	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7570695	0.84[AFR][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:127 , 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	chr2:54838600-54845600	Strong transcription	GM12878-XiMat	blood
3	chr2:54838800-54845800	Strong transcription	Primary B cells from cord blood	blood
4	chr2:54838800-54845800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:54838800-54846200	Enhancers	Right Atrium	heart
6	chr2:54838800-54848800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:54838800-54860200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:54838800-54893400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:54839000-54846800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:54839000-54848200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr2:54839000-54864200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:54839200-54845600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:54839200-54845600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:54839200-54845600	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr2:54839200-54845800	Strong transcription	Colonic Mucosa	Colon
16	chr2:54839200-54846800	Genic enhancers	Liver	Liver
17	chr2:54839200-54848600	Genic enhancers	Left Ventricle	heart
18	chr2:54839200-54861800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:54839200-54866000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:54839400-54853000	Strong transcription	Fetal Intestine Large	intestine
21	chr2:54839400-54895000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:54839600-54852400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:54839600-54862600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:54839800-54846800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr2:54839800-54847200	Genic enhancers	Fetal Lung	lung
26	chr2:54840800-54845600	Strong transcription	Dnd41	blood
27	chr2:54840800-54861400	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:54841000-54861400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:54841000-54861400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:54841200-54845600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:54841200-54846800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:54841200-54847200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:54841200-54861200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:54841200-54897800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:54841600-54845600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:54841600-54845600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr2:54841600-54845600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:54841600-54845600	Strong transcription	Duodenum Mucosa	Duodenum
39	chr2:54841600-54845600	Strong transcription	NHDF-Ad	bronchial
40	chr2:54841600-54845600	Strong transcription	NHLF	lung
41	chr2:54841600-54845800	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:54841600-54852400	Strong transcription	HSMMtube	muscle
43	chr2:54841600-54856200	Strong transcription	Hela-S3	cervix
44	chr2:54841600-54857000	Strong transcription	HSMM	muscle
45	chr2:54841800-54845800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:54841800-54845800	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr2:54841800-54847000	Strong transcription	HMEC	breast
48	chr2:54841800-54857000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr2:54841800-54860000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:54841800-54860000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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