Variant report

Variant	rs10489
Chromosome Location	chr3:69151152-69151153
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:69143722..69145244-chr3:69149402..69151807,2	K562	blood:
2	chr3:69061746..69063360-chr3:69150145..69151694,2	K562	blood:
3	chr3:69138840..69141310-chr3:69150694..69152337,2	MCF-7	breast:
4	chr3:69142415..69145222-chr3:69150307..69152771,2	K562	blood:
5	chr3:69133360..69135873-chr3:69150773..69153326,2	K562	blood:

Variant related genes	Relation type
ENSG00000163378	Chromatin interaction
ENSG00000244513	Chromatin interaction
ENSG00000144746	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1051901	0.93[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap];0.80[ASN][1000 genomes]
rs1131960	0.93[GIH][hapmap]
rs13090606	0.93[CHB][hapmap]
rs17005366	0.93[GIH][hapmap]
rs2009602	0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2271122	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs2292199	0.93[CHB][hapmap]
rs3772979	0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs3772980	0.82[ASW][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.94[MKK][hapmap];0.95[YRI][hapmap];0.80[ASN][1000 genomes]
rs3796213	0.93[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.80[ASN][1000 genomes]
rs3796214	0.93[GIH][hapmap]
rs3821562	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs3821564	0.80[ASN][1000 genomes]
rs3853157	0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs6549181	0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs6549184	1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6777032	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs72924853	0.80[ASN][1000 genomes]
rs72924854	0.80[ASN][1000 genomes]
rs73835726	0.80[ASN][1000 genomes]
rs7614224	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7621394	0.80[ASN][1000 genomes]
rs7621929	0.80[ASN][1000 genomes]
rs7625579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627893	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629932	0.80[ASN][1000 genomes]
rs9813514	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876933	chr3:69059023-69227379	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv876934	chr3:69111512-69166895	Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69135200-69155200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:69135800-69155800	Weak transcription	Fetal Kidney	kidney
3	chr3:69136800-69156400	Weak transcription	Fetal Brain Male	brain
4	chr3:69139800-69154600	Weak transcription	A549	lung
5	chr3:69141600-69151400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:69141600-69151600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:69141600-69152400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:69142000-69160400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:69142200-69153400	Weak transcription	Fetal Brain Female	brain
10	chr3:69142400-69152200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:69143600-69151200	Weak transcription	Colonic Mucosa	Colon
12	chr3:69143600-69152600	Weak transcription	Ovary	ovary
13	chr3:69143600-69152800	Weak transcription	Brain Germinal Matrix	brain
14	chr3:69143600-69160200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:69144200-69151200	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr3:69144200-69153000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:69145600-69151600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:69145600-69153600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:69145600-69160200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:69145800-69153400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:69145800-69160200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:69146200-69160200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:69146600-69151200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:69147200-69151600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:69147400-69160200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:69147800-69151200	Enhancers	Fetal Heart	heart
27	chr3:69147800-69152800	Weak transcription	Psoas Muscle	Psoas
28	chr3:69147800-69153600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:69148000-69153800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
30	chr3:69148600-69153800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:69148600-69155200	Strong transcription	Primary B cells from cord blood	blood
32	chr3:69148600-69155800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr3:69148800-69151600	Enhancers	Right Atrium	heart
34	chr3:69148800-69151800	Strong transcription	Fetal Intestine Small	intestine
35	chr3:69148800-69153400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:69148800-69153400	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr3:69148800-69153800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr3:69148800-69154000	Strong transcription	Fetal Muscle Leg	muscle
39	chr3:69148800-69155600	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr3:69148800-69155600	Strong transcription	GM12878-XiMat	blood
41	chr3:69148800-69155800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr3:69148800-69155800	Strong transcription	Dnd41	blood
43	chr3:69149000-69153200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:69149000-69154800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:69149200-69151200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:69149200-69151800	Strong transcription	Fetal Stomach	stomach
47	chr3:69149200-69152600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:69149200-69152800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:69149200-69154200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr3:69149200-69155400	Strong transcription	Fetal Thymus	thymus

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