Variant report

Variant	rs28569147
Chromosome Location	chr2:99074737-99074738
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99061382..99063642-chr2:99073429..99075733,2	MCF-7	breast:
2	chr2:99060406..99063375-chr2:99071149..99075402,6	MCF-7	breast:
3	chr2:99073761..99075633-chr2:99083363..99085810,2	MCF-7	breast:
4	chr2:99064982..99066484-chr2:99074260..99077190,2	MCF-7	breast:
5	chr2:99066884..99071356-chr2:99073843..99078046,5	MCF-7	breast:
6	chr2:99074297..99077605-chr2:99081893..99085320,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000040933	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10184555	1.00[AMR][1000 genomes]
rs13007839	0.94[AFR][1000 genomes]
rs13395005	1.00[AMR][1000 genomes]
rs13429817	1.00[AMR][1000 genomes]
rs17021866	1.00[AMR][1000 genomes]
rs17031804	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17031889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17031912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17031975	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17032010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17032806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17032843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17032847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17032916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9631039	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1006328	chr2:98977192-99210376	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1007244	chr2:99063753-99136472	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99063600-99075600	Weak transcription	Brain Germinal Matrix	brain
2	chr2:99065600-99079600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:99065600-99079600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr2:99066200-99075800	Weak transcription	Psoas Muscle	Psoas
5	chr2:99066800-99075400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:99068800-99075200	Weak transcription	Right Ventricle	heart
7	chr2:99068800-99079800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:99069600-99075600	Weak transcription	Brain Angular Gyrus	brain
9	chr2:99071200-99075200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:99071200-99077200	Weak transcription	Fetal Muscle Leg	muscle
11	chr2:99071200-99079600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:99071200-99079800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:99071400-99076800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:99071600-99075000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:99071600-99075000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:99071600-99075200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:99071600-99078000	Weak transcription	Fetal Lung	lung
18	chr2:99071600-99080200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr2:99071800-99075200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:99071800-99075400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr2:99071800-99076800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:99072000-99075400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:99072000-99075800	Weak transcription	Colonic Mucosa	Colon
24	chr2:99072000-99076400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:99072000-99079600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:99072200-99075200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:99072200-99075200	Weak transcription	Esophagus	oesophagus
28	chr2:99072200-99075200	Weak transcription	Right Atrium	heart
29	chr2:99072200-99075800	Genic enhancers	Fetal Thymus	thymus
30	chr2:99072200-99076400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr2:99072200-99081200	Weak transcription	Fetal Brain Male	brain
32	chr2:99072200-99083000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr2:99072200-99086200	Weak transcription	Fetal Intestine Small	intestine
34	chr2:99072400-99074800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:99072400-99075400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:99072400-99075400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:99072400-99075400	Weak transcription	Lung	lung
38	chr2:99072400-99075600	Genic enhancers	Primary T cells from cord blood	blood
39	chr2:99072400-99075800	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr2:99072400-99078000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr2:99072400-99078000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr2:99072400-99079800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:99072400-99095000	Weak transcription	Fetal Intestine Large	intestine
44	chr2:99072600-99075200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:99072600-99075200	Weak transcription	Spleen	Spleen
46	chr2:99072600-99075200	Weak transcription	HMEC	breast
47	chr2:99072600-99075400	Enhancers	Duodenum Mucosa	Duodenum
48	chr2:99072600-99075400	Weak transcription	Pancreas	Pancrea
49	chr2:99072600-99075400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:99072600-99075600	Genic enhancers	Primary T helper cells PMA-I stimulated	--

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