Variant report

Variant	rs323873
Chromosome Location	chr3:51993725-51993726
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51992685..51994681-chr3:51997289..51999303,2	MCF-7	breast:
2	chr3:51988009..51992311-chr3:51992660..51997455,6	K562	blood:
3	chr3:51992447..51994551-chr3:51995327..51997429,2	K562	blood:

Variant related genes	Relation type
ENSG00000090097	Chromatin interaction
ENSG00000180929	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11926611	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1566941	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1876052	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs188953	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2015691	1.00[MEX][hapmap];0.81[MKK][hapmap];0.90[AMR][1000 genomes]
rs2271069	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323858	1.00[MEX][hapmap]
rs323863	1.00[MEX][hapmap]
rs323864	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs323865	0.82[LWK][hapmap]
rs323868	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323874	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323879	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323881	1.00[ASN][1000 genomes]
rs323885	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323886	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs323887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323892	1.00[MEX][hapmap];0.81[MKK][hapmap]
rs323893	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323894	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs323895	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323897	1.00[MEX][hapmap];0.81[MKK][hapmap];0.90[AMR][1000 genomes]
rs323898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3755797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3774344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs379462	0.86[ASW][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes]
rs380788	0.90[AMR][1000 genomes]
rs404527	0.90[AMR][1000 genomes]
rs411209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4416372	0.86[CHB][hapmap]
rs4986825	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56715917	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61087263	0.89[ASN][1000 genomes]
rs6446166	0.85[ASN][1000 genomes]
rs72964028	0.90[AMR][1000 genomes]
rs72964029	0.80[AMR][1000 genomes]
rs7432986	1.00[MEX][hapmap]
rs7614743	0.89[ASN][1000 genomes]
rs9833784	0.82[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv876781	chr3:51985664-52009612	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv876782	chr3:51985664-52022779	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	nsv876783	chr3:51987224-52009612	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv876784	chr3:51987224-52013242	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51988400-52000600	Weak transcription	Hela-S3	cervix
2	chr3:51989400-51997000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:51990600-52000200	Weak transcription	NHDF-Ad	bronchial
4	chr3:51990600-52000400	Weak transcription	Small Intestine	intestine
5	chr3:51990600-52000400	Weak transcription	HUVEC	blood vessel
6	chr3:51990600-52000800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:51990800-51995000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:51990800-51996000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:51990800-51997200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:51990800-51999600	Weak transcription	NH-A	brain
11	chr3:51990800-52000400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:51991000-51994800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:51991000-51995600	Weak transcription	Right Atrium	heart
14	chr3:51991000-51995800	Strong transcription	Fetal Stomach	stomach
15	chr3:51991000-51995800	Weak transcription	Psoas Muscle	Psoas
16	chr3:51991000-51996000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:51991000-51996400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:51991000-51996600	Weak transcription	Fetal Brain Male	brain
19	chr3:51991000-51997000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:51991000-51997000	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr3:51991000-51997400	Strong transcription	NHLF	lung
22	chr3:51991000-51999600	Weak transcription	Colonic Mucosa	Colon
23	chr3:51991000-51999600	Weak transcription	HMEC	breast
24	chr3:51991000-51999800	Weak transcription	NHEK	skin
25	chr3:51991000-52000200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:51991000-52000400	Weak transcription	Stomach Mucosa	stomach
27	chr3:51991000-52000600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:51991200-51994800	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr3:51991200-51995000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:51991200-51995200	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:51991200-51995800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:51991200-51997400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:51991200-51997800	Genic enhancers	Brain Cingulate Gyrus	brain
34	chr3:51991200-52000000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:51991200-52000400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:51991200-52000400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:51991400-51995200	Strong transcription	Fetal Intestine Small	intestine
38	chr3:51991400-51995200	Strong transcription	Fetal Muscle Leg	muscle
39	chr3:51991400-51995400	Strong transcription	Fetal Brain Female	brain
40	chr3:51991400-51996800	Weak transcription	Fetal Heart	heart
41	chr3:51991400-51997000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:51991400-51997600	Genic enhancers	Brain Hippocampus Middle	brain
43	chr3:51991400-52000200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:51991600-51994400	Strong transcription	Fetal Intestine Large	intestine
45	chr3:51991600-51994600	Strong transcription	Right Ventricle	heart
46	chr3:51991600-51995000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:51991600-51995000	Strong transcription	Spleen	Spleen
48	chr3:51991600-51995200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:51991600-51995200	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:51991600-51995400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links