Variant report

Variant	rs13431271
Chromosome Location	chr2:58276164-58276165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58274389..58277128-chr2:58466604..58469335,2	K562	blood:
2	chr2:58131028..58133565-chr2:58275828..58277987,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273063	Chromatin interaction
ENSG00000115392	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10164499	0.93[MKK][hapmap]
rs10165760	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10174202	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10176681	0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10176942	0.89[AMR][1000 genomes]
rs10178025	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10182762	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10187411	0.90[LWK][hapmap];1.00[MKK][hapmap];0.87[AMR][1000 genomes]
rs10203014	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1025755	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10518852	1.00[MKK][hapmap]
rs11883874	0.82[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11891477	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11892302	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11903212	0.80[MKK][hapmap]
rs13382369	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13394820	0.92[AFR][1000 genomes]
rs13405281	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13410500	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs13419989	0.85[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1371213	0.89[AMR][1000 genomes]
rs2165100	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2165103	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2312486	0.89[AMR][1000 genomes]
rs28521626	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4459722	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57112138	0.89[AMR][1000 genomes]
rs57597086	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs58470176	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs60364084	0.89[AMR][1000 genomes]
rs6718190	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs716758	0.89[AMR][1000 genomes]
rs72949131	0.87[AMR][1000 genomes]
rs72949137	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72949158	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72951042	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72951048	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72951056	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73944804	0.86[AFR][1000 genomes]
rs7563225	0.97[MKK][hapmap]
rs7563312	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7569731	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7574578	0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs7574694	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7590976	1.00[MEX][hapmap];0.85[MKK][hapmap]
rs7600213	0.91[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9973345	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9973928	0.80[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv999591	chr2:58214871-58316147	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv582097	chr2:58266099-58346966	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv874201	chr2:58269871-58350504	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv874202	chr2:58269871-58375688	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58272600-58277400	Active TSS	GM12878-XiMat	blood
2	chr2:58274600-58276400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:58274600-58283600	Weak transcription	Gastric	stomach
4	chr2:58274600-58298600	Weak transcription	Spleen	Spleen
5	chr2:58274600-58302400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:58274800-58276200	Flanking Active TSS	HUVEC	blood vessel
7	chr2:58274800-58276400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr2:58274800-58282200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:58274800-58296400	Weak transcription	Ovary	ovary
10	chr2:58274800-58296600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:58274800-58302200	Weak transcription	Aorta	Aorta
12	chr2:58274800-58317400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:58275000-58276800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:58275000-58278600	Weak transcription	Brain Substantia Nigra	brain
15	chr2:58275000-58280200	Weak transcription	Fetal Lung	lung
16	chr2:58275000-58282000	Weak transcription	Primary T cells from cord blood	blood
17	chr2:58275000-58282200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:58275000-58282200	Weak transcription	Fetal Muscle Leg	muscle
19	chr2:58275000-58282200	Weak transcription	Left Ventricle	heart
20	chr2:58275000-58283800	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr2:58275000-58285000	Weak transcription	Fetal Intestine Large	intestine
22	chr2:58275000-58285000	Weak transcription	Placenta	Placenta
23	chr2:58275000-58285400	Weak transcription	Fetal Thymus	thymus
24	chr2:58275000-58287800	Weak transcription	Fetal Kidney	kidney
25	chr2:58275000-58290800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:58275000-58290800	Weak transcription	Thymus	Thymus
27	chr2:58275000-58291000	Weak transcription	HSMM	muscle
28	chr2:58275000-58297600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:58275000-58302600	Weak transcription	Esophagus	oesophagus
30	chr2:58275000-58302800	Weak transcription	Fetal Stomach	stomach
31	chr2:58275000-58305600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:58275000-58317400	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:58275000-58321600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:58275000-58326600	Weak transcription	Pancreas	Pancrea
35	chr2:58275200-58283600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:58275400-58276200	Transcr. at gene 5' and 3'	A549	lung
37	chr2:58275400-58276200	Enhancers	HepG2	liver
38	chr2:58275400-58278600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:58275400-58281800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:58275400-58283200	Weak transcription	Adipose Nuclei	Adipose
41	chr2:58275400-58283400	Weak transcription	Primary B cells from cord blood	blood
42	chr2:58275400-58283800	Weak transcription	Right Ventricle	heart
43	chr2:58275400-58290000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr2:58275400-58290600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:58275400-58290600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr2:58275400-58290800	Weak transcription	Brain Anterior Caudate	brain
47	chr2:58275400-58291000	Weak transcription	NH-A	brain
48	chr2:58275400-58294400	Weak transcription	Fetal Intestine Small	intestine
49	chr2:58275600-58276200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr2:58275600-58276200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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