Variant report

Variant	rs4129598
Chromosome Location	chr12:104620638-104620639
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104611588..104614072-chr12:104619313..104622128,3	K562	blood:
2	chr12:104611527..104621556-chr12:104677756..104684608,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10400561	0.81[ASN][1000 genomes]
rs10507174	0.84[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];1.00[MKK][hapmap]
rs10507175	0.85[CEU][hapmap];0.85[CHB][hapmap];0.87[MEX][hapmap]
rs10735392	1.00[ASW][hapmap];0.86[CEU][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes]
rs10735393	0.86[CEU][hapmap]
rs10745995	1.00[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs10745996	1.00[ASW][hapmap];0.86[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs10778311	0.81[JPT][hapmap]
rs10778316	0.88[JPT][hapmap]
rs10778318	0.81[JPT][hapmap]
rs10861169	1.00[JPT][hapmap]
rs10861180	0.90[JPT][hapmap]
rs10861204	0.86[CEU][hapmap]
rs11111898	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs11111943	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11111955	0.87[ASN][1000 genomes]
rs11111960	0.81[JPT][hapmap]
rs11111963	0.81[JPT][hapmap]
rs12422505	0.85[CHB][hapmap]
rs12423844	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs12424869	0.88[JPT][hapmap]
rs12424943	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs12426862	0.85[CHB][hapmap]
rs12427339	0.85[CEU][hapmap];0.80[CHD][hapmap]
rs12582966	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs12825521	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs17035153	1.00[MKK][hapmap]
rs17035324	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17035504	1.00[MKK][hapmap]
rs17192854	0.85[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];1.00[MKK][hapmap]
rs17805748	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs17805766	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs4131750	0.85[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap]
rs4131752	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs4246264	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4246269	0.86[CEU][hapmap]
rs4246271	0.86[CEU][hapmap]
rs4340124	0.85[CEU][hapmap]
rs4388968	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4406890	0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs4475991	0.83[CHD][hapmap];0.89[JPT][hapmap]
rs4502051	0.81[AMR][1000 genomes]
rs4545635	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4614534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4630362	0.84[CEU][hapmap]
rs4964226	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4964227	0.93[CEU][hapmap]
rs4964228	0.93[CEU][hapmap]
rs4964257	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4964260	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4964270	0.87[ASN][1000 genomes]
rs4964271	0.91[ASN][1000 genomes]
rs4964288	1.00[ASW][hapmap];0.86[CEU][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap]
rs4964627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4964632	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4964728	0.83[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs4964735	0.81[JPT][hapmap]
rs4964741	0.82[AMR][1000 genomes]
rs4964752	1.00[ASW][hapmap];0.86[CEU][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.81[AMR][1000 genomes]
rs4964761	1.00[ASW][hapmap];0.86[CEU][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.82[AMR][1000 genomes]
rs4964779	1.00[ASW][hapmap];0.86[CEU][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.81[AMR][1000 genomes]
rs61939222	0.81[ASN][1000 genomes]
rs6419386	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6539128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539137	0.83[CEU][hapmap]
rs7132418	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7138035	0.91[CEU][hapmap]
rs7138317	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7138523	0.81[JPT][hapmap]
rs7139336	0.82[AMR][1000 genomes]
rs7294997	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs7295413	0.84[ASN][1000 genomes]
rs7298613	0.81[AMR][1000 genomes]
rs7299866	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7305872	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7310505	0.90[JPT][hapmap]
rs7313063	0.83[CHD][hapmap];0.89[JPT][hapmap]
rs7314893	0.84[JPT][hapmap]
rs73177991	1.00[AFR][1000 genomes]
rs7342395	0.81[JPT][hapmap]
rs7957725	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7958851	0.92[ASN][1000 genomes]
rs7962423	0.86[CEU][hapmap]
rs7969351	0.81[AMR][1000 genomes]
rs7975161	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[ASN][1000 genomes]
rs7978101	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9739833	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
2	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4129598	NFYB	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104614000-104623400	Weak transcription	Right Atrium	heart
2	chr12:104615000-104625800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:104620000-104621600	Enhancers	NHEK	skin
4	chr12:104620600-104620800	Enhancers	NH-A	brain
5	chr12:104620600-104621000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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