Variant report

Variant	rs12640389
Chromosome Location	chr4:143652106-143652107
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143651955..143654079-chr4:143655734..143658142,2	MCF-7	breast:
2	chr4:143646473..143648911-chr4:143650261..143652367,2	MCF-7	breast:

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10024696	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1031104	1.00[CHB][hapmap];0.84[MEX][hapmap]
rs10857399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11100754	0.81[JPT][hapmap];0.88[EUR][1000 genomes]
rs11100760	0.81[EUR][1000 genomes]
rs11723982	0.90[ASN][1000 genomes]
rs11933763	0.94[EUR][1000 genomes]
rs11943397	0.90[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs11944455	0.81[CHB][hapmap]
rs12509304	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12644329	0.88[EUR][1000 genomes]
rs13117185	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13141925	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13435565	0.88[EUR][1000 genomes]
rs1364925	0.81[JPT][hapmap]
rs1373030	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1373031	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1373032	0.89[EUR][1000 genomes]
rs1441417	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1443183	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1443185	0.88[EUR][1000 genomes]
rs1443186	0.88[EUR][1000 genomes]
rs1443187	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1443191	0.81[JPT][hapmap]
rs1465962	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs167960	0.84[ASN][1000 genomes]
rs17016768	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs17016777	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17016779	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17016789	0.84[ASN][1000 genomes]
rs17732791	0.85[EUR][1000 genomes]
rs179508	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1822360	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1822361	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1822362	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1838082	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1867214	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1899565	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs191762	0.90[EUR][1000 genomes]
rs1965828	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1992417	0.84[EUR][1000 genomes]
rs1992418	0.84[EUR][1000 genomes]
rs2017146	0.81[JPT][hapmap]
rs2120158	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs2165820	0.80[JPT][hapmap]
rs2589994	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28420913	0.88[EUR][1000 genomes]
rs2874870	0.81[JPT][hapmap]
rs2874871	0.81[JPT][hapmap]
rs3113593	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs331939	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs331940	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs331942	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs331943	0.84[ASN][1000 genomes]
rs331945	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs331946	0.82[ASN][1000 genomes]
rs331947	0.82[ASN][1000 genomes]
rs331948	0.91[EUR][1000 genomes]
rs331949	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs331950	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs331951	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs331952	0.84[ASN][1000 genomes]
rs331953	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs331954	0.82[ASN][1000 genomes]
rs331956	0.82[ASN][1000 genomes]
rs331957	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs331958	0.82[ASN][1000 genomes]
rs331959	0.82[ASN][1000 genomes]
rs331960	0.82[ASN][1000 genomes]
rs331961	0.82[ASN][1000 genomes]
rs331962	0.82[ASN][1000 genomes]
rs331963	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs331964	0.82[ASN][1000 genomes]
rs331965	0.82[ASN][1000 genomes]
rs331966	0.86[EUR][1000 genomes]
rs34442253	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4690698	0.94[MEX][hapmap]
rs4690699	0.94[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs4690700	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4690725	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4690726	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4690727	0.84[ASN][1000 genomes]
rs56011189	0.81[ASN][1000 genomes]
rs6537124	0.84[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs6537127	0.83[EUR][1000 genomes]
rs6537129	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs6813458	0.87[EUR][1000 genomes]
rs6816424	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6819498	0.88[EUR][1000 genomes]
rs6830053	1.00[CHB][hapmap]
rs6831562	0.82[EUR][1000 genomes]
rs6831927	0.88[EUR][1000 genomes]
rs6839158	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6844306	0.88[EUR][1000 genomes]
rs6845583	0.88[EUR][1000 genomes]
rs6852570	0.91[EUR][1000 genomes]
rs72728641	0.81[ASN][1000 genomes]
rs72728654	0.86[ASN][1000 genomes]
rs72728667	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7376475	0.95[EUR][1000 genomes]
rs7656375	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs7663475	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7666140	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs7667183	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7688275	0.86[EUR][1000 genomes]
rs966457	0.90[EUR][1000 genomes]
rs978361	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830101	chr4:143518810-143684392	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv595606	chr4:143631691-143729595	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv880174	chr4:143639498-143848024	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143637200-143653000	Weak transcription	Left Ventricle	heart
2	chr4:143641600-143652800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:143642800-143664200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:143647400-143652200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr4:143648400-143653200	Enhancers	Dnd41	blood
6	chr4:143649000-143652800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:143650600-143655800	Weak transcription	Thymus	Thymus
8	chr4:143651000-143652600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:143651000-143664400	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links