Variant report

Variant	rs2236973
Chromosome Location	chr3:50474284-50474285
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50473646..50476114-chr3:50476289..50479526,3	MCF-7	breast:
2	chr3:50471606..50474364-chr3:50476758..50479663,3	K562	blood:
3	chr3:50473655..50474324-chr3:50587187..50588173,2	MCF-7	breast:
4	chr3:50386862..50388722-chr3:50472468..50474330,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114388	Chromatin interaction
ENSG00000114395	Chromatin interaction
ENSG00000272104	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1107265	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130250	0.81[EUR][1000 genomes]
rs12490042	0.94[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs12492113	0.82[CEU][hapmap]
rs12494849	0.86[ASW][hapmap];0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13087550	0.94[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs13099869	0.82[EUR][1000 genomes]
rs1467913	0.80[ASW][hapmap];0.89[CEU][hapmap]
rs1467914	0.86[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2073496	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2073499	0.85[ASW][hapmap]
rs2233474	0.93[ASW][hapmap]
rs2236951	0.86[ASW][hapmap];0.87[MEX][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs2236953	0.94[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2236954	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2236955	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2236956	0.94[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs2236957	1.00[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2236958	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2236959	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs2236961	0.94[CEU][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs2236962	0.85[EUR][1000 genomes]
rs2236963	0.94[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2236964	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2236965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2236967	0.94[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2236968	0.94[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs2236971	0.92[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs2236975	0.94[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs2236979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236981	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2236983	0.82[EUR][1000 genomes]
rs2236984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2236987	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2236988	0.94[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs2282752	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2282753	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2282754	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2282756	0.94[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs2282758	0.94[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs2282760	0.82[EUR][1000 genomes]
rs2282762	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2298955	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34762184	0.82[CEU][hapmap]
rs35986136	0.82[CEU][hapmap]
rs4688719	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs4688720	0.82[EUR][1000 genomes]
rs6446206	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6786523	0.80[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6787890	0.94[CEU][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs6792502	0.89[CEU][hapmap]
rs6807916	0.82[CEU][hapmap]
rs71326932	0.89[EUR][1000 genomes]
rs734767	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs743756	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs743757	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs743857	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs750510	0.84[CEU][hapmap]
rs762895	0.94[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs762897	0.94[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs762898	0.94[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs763030	0.89[CEU][hapmap]
rs916217	0.94[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs929047	0.94[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs9835537	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9867588	0.88[CEU][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
6	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
8	nsv876773	chr3:50302830-50480131	Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
9	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
10	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
11	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
12	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
15	esv3445182	chr3:50458687-50496660	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
16	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2236973	ALS2CL	cis	parietal	SCAN
rs2236973	APEH	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50465600-50485800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:50465800-50487000	Weak transcription	Fetal Intestine Small	intestine
3	chr3:50468200-50474600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:50468800-50478800	Weak transcription	Fetal Lung	lung
5	chr3:50468800-50480200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:50469000-50475800	Weak transcription	Brain Anterior Caudate	brain
7	chr3:50470200-50479000	Weak transcription	Left Ventricle	heart
8	chr3:50471200-50479800	Enhancers	Fetal Heart	heart
9	chr3:50471600-50479600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:50471800-50475200	Weak transcription	Spleen	Spleen
11	chr3:50471800-50477800	Weak transcription	Gastric	stomach
12	chr3:50472000-50474400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:50472000-50475400	Weak transcription	Lung	lung
14	chr3:50472200-50477000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:50473200-50477800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr3:50473200-50483800	Enhancers	Fetal Muscle Leg	muscle
17	chr3:50473800-50476000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:50473800-50476000	Enhancers	Right Atrium	heart
19	chr3:50474000-50476000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:50474000-50479200	Weak transcription	Right Ventricle	heart
21	chr3:50474000-50487400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:50474200-50475200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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