Variant report

Variant	rs10179509
Chromosome Location	chr2:134253212-134253213
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:134251643..134253707-chr2:134255624..134257629,2	MCF-7	breast:
2	chr2:134250533..134253276-chr2:134255115..134256615,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10172908	1.00[EUR][1000 genomes]
rs10176630	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10180776	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10182352	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10204302	1.00[EUR][1000 genomes]
rs11904353	1.00[EUR][1000 genomes]
rs13383175	1.00[EUR][1000 genomes]
rs13383603	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs13396221	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13402934	1.00[EUR][1000 genomes]
rs13406195	1.00[EUR][1000 genomes]
rs13406470	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs13410388	1.00[EUR][1000 genomes]
rs13419194	0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13432659	1.00[EUR][1000 genomes]
rs16825509	0.80[YRI][hapmap]
rs1897430	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs1897431	1.00[EUR][1000 genomes]
rs28420171	1.00[EUR][1000 genomes]
rs28634361	1.00[EUR][1000 genomes]
rs6718180	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6727895	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134240000-134262400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:134246400-134262400	Weak transcription	Gastric	stomach
3	chr2:134247800-134254800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:134248000-134262000	Weak transcription	NHLF	lung
5	chr2:134248200-134256600	Weak transcription	NHEK	skin
6	chr2:134248400-134255000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:134249000-134254400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:134249000-134254600	Weak transcription	NHDF-Ad	bronchial
9	chr2:134250200-134257200	Enhancers	Fetal Intestine Small	intestine
10	chr2:134250400-134255800	Enhancers	Liver	Liver
11	chr2:134250800-134257800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:134251400-134253600	Enhancers	Fetal Intestine Large	intestine
13	chr2:134251600-134254000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:134251600-134261400	Weak transcription	Right Atrium	heart
15	chr2:134252200-134253400	Enhancers	Brain Angular Gyrus	brain
16	chr2:134252200-134254000	Enhancers	Duodenum Mucosa	Duodenum
17	chr2:134252200-134257000	Enhancers	Fetal Kidney	kidney
18	chr2:134252600-134254800	Enhancers	Brain Germinal Matrix	brain
19	chr2:134252600-134255800	Enhancers	Brain Substantia Nigra	brain
20	chr2:134252600-134257000	Enhancers	Fetal Brain Female	brain
21	chr2:134252600-134257600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr2:134252800-134253600	Enhancers	Fetal Lung	lung
23	chr2:134252800-134254000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:134252800-134254600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:134252800-134255400	Enhancers	Brain Anterior Caudate	brain
26	chr2:134252800-134255400	Enhancers	Brain Cingulate Gyrus	brain
27	chr2:134252800-134255600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:134252800-134255800	Enhancers	Brain Hippocampus Middle	brain
29	chr2:134253000-134253400	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr2:134253000-134253400	Enhancers	Fetal Stomach	stomach
31	chr2:134253000-134253400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr2:134253000-134253400	Enhancers	Small Intestine	intestine
33	chr2:134253000-134253800	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr2:134253000-134254000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:134253200-134253800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:134253200-134254600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:134253200-134255000	Enhancers	Fetal Brain Male	brain
38	chr2:134253200-134255000	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:134253200-134255000	Weak transcription	Left Ventricle	heart
40	chr2:134253200-134255200	Weak transcription	Stomach Mucosa	stomach
41	chr2:134253200-134255800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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