Variant report

Variant	rs13409277
Chromosome Location	chr2:54701860-54701861
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54699717..54702089-chr2:54703143..54705442,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10153583	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10153704	0.89[EUR][1000 genomes]
rs12328732	0.96[EUR][1000 genomes]
rs13391816	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13391936	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13403941	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17045932	0.89[EUR][1000 genomes]
rs28380233	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28441070	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28682325	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28698551	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv874150	chr2:54684557-54755229	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv874151	chr2:54684557-54761329	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1004645	chr2:54686497-54718440	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1008888	chr2:54690695-54715300	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3693290	chr2:54693204-54707562	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv438348	chr2:54693204-54714066	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv817939	chr2:54693204-54718181	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54696800-54703600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:54697200-54707200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:54697200-54709600	Weak transcription	Placenta	Placenta
4	chr2:54698800-54702600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:54698800-54702600	Weak transcription	Gastric	stomach
6	chr2:54698800-54702600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:54698800-54702600	Weak transcription	Spleen	Spleen
8	chr2:54698800-54703400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:54698800-54705200	Weak transcription	Lung	lung
10	chr2:54698800-54707200	Weak transcription	Pancreas	Pancrea
11	chr2:54699000-54702400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:54699000-54702600	Weak transcription	Right Atrium	heart
13	chr2:54699000-54706000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:54699200-54706200	Weak transcription	HUVEC	blood vessel
15	chr2:54699600-54703200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:54699600-54706600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:54699600-54709200	Weak transcription	Aorta	Aorta
18	chr2:54699800-54702400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:54699800-54702400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:54699800-54703200	Weak transcription	Fetal Brain Female	brain
21	chr2:54699800-54707000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:54699800-54709600	Weak transcription	Osteobl	bone
23	chr2:54700000-54702000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:54700000-54702400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:54700000-54702400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:54700000-54702400	Weak transcription	NHDF-Ad	bronchial
27	chr2:54700000-54702600	Weak transcription	HepG2	liver
28	chr2:54700200-54703400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:54700400-54703600	Weak transcription	NHLF	lung
30	chr2:54700600-54705600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:54700600-54705600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:54701000-54702200	Enhancers	Placenta Amnion	Placenta Amnion
33	chr2:54701000-54702600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:54701000-54703400	Enhancers	Psoas Muscle	Psoas
35	chr2:54701000-54703800	Enhancers	Fetal Muscle Leg	muscle
36	chr2:54701000-54703800	Genic enhancers	Left Ventricle	heart
37	chr2:54701000-54703800	Enhancers	Ovary	ovary
38	chr2:54701200-54702600	Weak transcription	Brain Angular Gyrus	brain
39	chr2:54701200-54705200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:54701200-54707200	Weak transcription	Fetal Brain Male	brain
41	chr2:54701400-54702400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:54701400-54702400	Weak transcription	Adipose Nuclei	Adipose
43	chr2:54701400-54702400	Weak transcription	Brain Substantia Nigra	brain
44	chr2:54701400-54702400	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:54701400-54702600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:54701400-54703200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr2:54701400-54703800	Genic enhancers	HSMM	muscle
48	chr2:54701400-54704800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:54701400-54705000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:54701400-54709800	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links