Variant report

Variant	rs900690
Chromosome Location	chr3:47462200-47462201
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47460494..47462590-chr3:47469043..47471406,2	K562	blood:
2	chr3:47421407..47424002-chr3:47461205..47462744,2	K562	blood:
3	chr3:47461509..47464905-chr3:47467197..47468812,4	K562	blood:
4	chr3:47462059..47463174-chr3:47516921..47518022,7	K562	blood:
5	chr3:47459970..47462496-chr3:47555005..47557478,2	K562	blood:
6	chr3:47462092..47463205-chr3:47555080..47555844,5	K562	blood:
7	chr3:47450663..47453382-chr3:47461645..47463185,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000076201	Chromatin interaction
ENSG00000260236	Chromatin interaction
ENSG00000114650	Chromatin interaction
ENSG00000163832	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1024036	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs1038393	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs10865947	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1091068	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11707272	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12491029	1.00[YRI][hapmap]
rs12631697	1.00[EUR][1000 genomes]
rs13077134	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs1531874	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1872165	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1874264	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2170814	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs295431	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295432	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295434	1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295443	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs295444	1.00[EUR][1000 genomes]
rs295445	1.00[EUR][1000 genomes]
rs295448	1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295450	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295451	1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295453	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295454	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295455	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295456	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295457	1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295459	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs448018	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858812	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858823	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858855	1.00[AMR][1000 genomes]
rs4858896	1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6442066	1.00[EUR][1000 genomes]
rs6442068	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442069	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs648226	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6772449	0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs6778673	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6778687	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs6783591	1.00[EUR][1000 genomes]
rs6785538	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787210	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs6788978	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789730	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808117	1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs7372780	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7612191	0.87[AMR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621853	0.87[AMR][1000 genomes]
rs7630154	1.00[EUR][1000 genomes]
rs7639121	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7644043	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs807930	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs807933	1.00[EUR][1000 genomes]
rs900688	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900689	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900691	1.00[EUR][1000 genomes]
rs900692	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900693	0.89[YRI][hapmap]
rs900694	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs903538	1.00[YRI][hapmap]
rs924009	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs9823599	0.85[AMR][1000 genomes]
rs9826488	1.00[EUR][1000 genomes]
rs9828124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9861247	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]
rs9869489	1.00[EUR][1000 genomes]

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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:142 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47426200-47462400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:47437800-47462800	Weak transcription	Fetal Brain Male	brain
3	chr3:47441000-47476800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:47441400-47462400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:47445000-47462400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:47445000-47462800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:47445600-47462800	Strong transcription	Fetal Brain Female	brain
8	chr3:47446000-47462200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:47446000-47462800	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:47446200-47462800	Strong transcription	Dnd41	blood
11	chr3:47446400-47462800	Strong transcription	Colonic Mucosa	Colon
12	chr3:47446600-47462800	Strong transcription	Brain Germinal Matrix	brain
13	chr3:47446800-47462200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr3:47447000-47462400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:47447000-47462400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:47447000-47462400	Weak transcription	Fetal Heart	heart
17	chr3:47447000-47462400	Strong transcription	NHLF	lung
18	chr3:47447000-47462600	Strong transcription	Fetal Stomach	stomach
19	chr3:47447200-47462200	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:47447200-47462400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:47447400-47462200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr3:47447400-47462400	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr3:47447400-47462600	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:47447800-47462400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:47447800-47462400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:47447800-47462400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr3:47447800-47462600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:47447800-47462800	Weak transcription	Right Atrium	heart
29	chr3:47448200-47462400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:47448200-47462400	Strong transcription	Left Ventricle	heart
31	chr3:47448200-47462400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr3:47448200-47462600	Strong transcription	Fetal Thymus	thymus
33	chr3:47448400-47462200	Strong transcription	Ovary	ovary
34	chr3:47448400-47462400	Strong transcription	Lung	lung
35	chr3:47448400-47463200	Strong transcription	Gastric	stomach
36	chr3:47448400-47466000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:47448600-47462400	Strong transcription	Pancreas	Pancrea
38	chr3:47448600-47462400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr3:47448600-47462800	Strong transcription	Fetal Intestine Small	intestine
40	chr3:47448800-47462800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:47448800-47463200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:47449000-47462400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:47449400-47462800	Strong transcription	Esophagus	oesophagus
44	chr3:47450400-47484800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:47450600-47462200	Strong transcription	Placenta	Placenta
46	chr3:47451000-47462400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:47451200-47462800	Weak transcription	HSMM	muscle
48	chr3:47451400-47466400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr3:47452600-47462600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:47453000-47462400	Weak transcription	HUVEC	blood vessel

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