Variant report

Variant	rs13398961
Chromosome Location	chr2:39752075-39752076
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39750470..39752970-chr2:39756347..39759099,3	K562	blood:
2	chr2:39749162..39751923-chr2:39751985..39754949,2	MCF-7	breast:
3	chr2:39751067..39752674-chr2:39760072..39761587,2	MCF-7	breast:
4	chr2:39750470..39752970-chr2:39756347..39759099,2	K562	blood:
5	chr2:39741137..39743112-chr2:39751728..39753579,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10182967	1.00[EUR][1000 genomes]
rs10183115	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10185836	1.00[EUR][1000 genomes]
rs10194751	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10207329	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13410300	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13414845	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13415549	1.00[EUR][1000 genomes]
rs13430261	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28667057	1.00[EUR][1000 genomes]
rs28885808	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6742173	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39744200-39753200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:39748400-39753600	Enhancers	Psoas Muscle	Psoas
3	chr2:39748600-39753400	Enhancers	Left Ventricle	heart
4	chr2:39748800-39753000	Enhancers	Stomach Smooth Muscle	stomach
5	chr2:39749000-39752200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr2:39749400-39757200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:39749400-39758000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:39749400-39761000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:39749600-39753400	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr2:39749800-39752600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:39749800-39752600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:39749800-39753000	Enhancers	HSMM	muscle
13	chr2:39749800-39753400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:39750000-39752400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:39750000-39752600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:39750000-39752600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:39750000-39752600	Enhancers	Hela-S3	cervix
18	chr2:39750000-39752600	Enhancers	NHLF	lung
19	chr2:39750000-39752800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:39750000-39761000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:39750200-39752600	Enhancers	NHDF-Ad	bronchial
22	chr2:39750200-39752800	Enhancers	NH-A	brain
23	chr2:39750200-39753400	Enhancers	Adipose Nuclei	Adipose
24	chr2:39750200-39753400	Enhancers	Fetal Heart	heart
25	chr2:39750400-39752600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr2:39750400-39752600	Enhancers	Aorta	Aorta
27	chr2:39750400-39753200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:39750400-39753400	Enhancers	Fetal Muscle Leg	muscle
29	chr2:39750600-39753000	Enhancers	Placenta	Placenta
30	chr2:39750600-39753400	Enhancers	Right Atrium	heart
31	chr2:39750600-39754400	Enhancers	HepG2	liver
32	chr2:39750800-39760200	Weak transcription	Gastric	stomach
33	chr2:39751200-39752400	Enhancers	Fetal Muscle Trunk	muscle
34	chr2:39751200-39752600	Enhancers	Fetal Stomach	stomach
35	chr2:39751200-39753000	Enhancers	Liver	Liver
36	chr2:39751200-39760400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:39751400-39752400	Weak transcription	Pancreas	Pancrea
38	chr2:39751400-39752400	Weak transcription	Stomach Mucosa	stomach
39	chr2:39751400-39752600	Enhancers	HMEC	breast
40	chr2:39751400-39752600	Enhancers	NHEK	skin
41	chr2:39751400-39752600	Enhancers	Osteobl	bone
42	chr2:39751400-39753000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:39751400-39753200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:39751400-39753400	Enhancers	A549	lung
45	chr2:39751400-39753600	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr2:39751400-39760200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:39751600-39752800	Weak transcription	K562	blood
48	chr2:39751600-39753000	Enhancers	Muscle Satellite Cultured Cells	--
49	chr2:39751600-39753400	Enhancers	HSMMtube	muscle
50	chr2:39751600-39757200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links