Variant report

Variant	rs12469788
Chromosome Location	chr2:173312955-173312956
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10497383	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs10497384	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs11883720	0.81[CEU][hapmap]
rs11896937	0.80[CEU][hapmap]
rs11897024	0.80[CEU][hapmap]
rs12473999	0.88[CEU][hapmap]
rs1574258	0.81[CEU][hapmap]
rs17286988	0.81[CEU][hapmap]
rs17676243	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs17676773	0.81[CEU][hapmap]
rs17677404	0.81[CEU][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap]
rs17727678	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs17727732	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs17739735	0.80[CEU][hapmap]
rs17739946	0.81[CEU][hapmap]
rs2272498	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs36002642	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3762620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3762621	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3792255	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs3792256	0.81[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.80[EUR][1000 genomes]
rs3828342	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs4972511	0.81[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap]
rs4972832	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs55726436	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6433358	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433359	0.81[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.80[EUR][1000 genomes]
rs6433360	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs6715294	0.80[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6717877	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718033	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728123	0.81[AMR][1000 genomes]
rs6728419	0.81[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap]
rs6731691	0.81[CEU][hapmap]
rs6755605	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs7565670	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594889	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173305000-173316800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:173306800-173316400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:173307200-173318600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:173307400-173313600	Weak transcription	Placenta	Placenta
5	chr2:173307400-173322400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:173307600-173313400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:173307600-173313600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:173307600-173313800	Weak transcription	Right Ventricle	heart
9	chr2:173307600-173314000	Enhancers	Duodenum Mucosa	Duodenum
10	chr2:173307600-173314600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:173307600-173314800	Weak transcription	Esophagus	oesophagus
12	chr2:173307600-173315600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr2:173307600-173321000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:173308000-173313800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:173308200-173313400	Weak transcription	HepG2	liver
16	chr2:173309000-173317000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:173309200-173315200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:173309400-173315600	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr2:173309600-173313000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:173309600-173313400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:173310000-173313200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:173310400-173313200	Enhancers	Primary T cells from cord blood	blood
23	chr2:173310400-173313200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:173310400-173314600	Enhancers	HMEC	breast
25	chr2:173310400-173318000	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr2:173310600-173314400	Enhancers	Fetal Intestine Small	intestine
27	chr2:173310600-173314600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:173310800-173313600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:173310800-173313600	Weak transcription	Left Ventricle	heart
30	chr2:173310800-173313600	Weak transcription	Right Atrium	heart
31	chr2:173310800-173314200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:173310800-173314600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:173310800-173314800	Weak transcription	Psoas Muscle	Psoas
34	chr2:173310800-173314800	Weak transcription	Spleen	Spleen
35	chr2:173310800-173317000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:173310800-173318200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:173310800-173318600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr2:173310800-173319800	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:173310800-173320000	Weak transcription	Lung	lung
40	chr2:173310800-173322400	Weak transcription	Thymus	Thymus
41	chr2:173311000-173316400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:173311400-173313000	Weak transcription	Fetal Lung	lung
43	chr2:173311400-173313600	Weak transcription	Gastric	stomach
44	chr2:173311400-173314000	Enhancers	Pancreas	Pancrea
45	chr2:173311400-173314400	Enhancers	Fetal Intestine Large	intestine
46	chr2:173311400-173315000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:173311400-173318000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr2:173311600-173314800	Weak transcription	NH-A	brain
49	chr2:173311600-173314800	Enhancers	NHEK	skin
50	chr2:173311600-173316000	Weak transcription	Monocytes-CD14+_RO01746	blood

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