Variant report

Variant	rs962393
Chromosome Location	chr6:119101336-119101337
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119095345..119097623-chr6:119099653..119102563,2	K562	blood:
2	chr6:119098916..119101415-chr6:119102887..119105983,3	K562	blood:
3	chr6:119099349..119102563-chr6:119103399..119106439,3	K562	blood:

Variant related genes	Relation type
ENSG00000225549	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10485389	0.86[ASN][1000 genomes]
rs11963765	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12191819	0.80[CHB][hapmap]
rs12197931	0.80[CHB][hapmap];0.95[LWK][hapmap];0.91[YRI][hapmap]
rs12203353	0.81[ASN][1000 genomes]
rs12203542	0.81[ASN][1000 genomes]
rs12206826	0.80[CHB][hapmap]
rs12210027	0.81[ASN][1000 genomes]
rs12214434	0.81[ASN][1000 genomes]
rs12216519	0.81[ASN][1000 genomes]
rs1407205	0.80[CHB][hapmap];0.91[YRI][hapmap]
rs17080604	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17080617	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17080626	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2005303	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2051056	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs2051057	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs2185560	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2295709	0.94[JPT][hapmap]
rs284914	0.80[CHB][hapmap];0.95[LWK][hapmap];0.91[YRI][hapmap]
rs376225	0.81[ASN][1000 genomes]
rs3798595	0.80[CHB][hapmap]
rs4946383	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs56895036	0.83[ASN][1000 genomes]
rs62424023	0.82[ASN][1000 genomes]
rs62424024	0.82[ASN][1000 genomes]
rs6909006	0.85[ASN][1000 genomes]
rs6910327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6910850	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs706971	0.80[CHB][hapmap]
rs72966811	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs768996	0.90[YRI][hapmap]
rs7740511	0.85[ASN][1000 genomes]
rs7741194	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7742473	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7742814	0.84[ASN][1000 genomes]
rs7745728	0.83[ASN][1000 genomes]
rs7750777	0.83[ASN][1000 genomes]
rs7758986	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7765824	0.85[ASN][1000 genomes]
rs794262	0.88[JPT][hapmap]
rs794607	0.80[CHB][hapmap]
rs794614	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs9320667	0.83[ASN][1000 genomes]
rs9374753	0.81[ASN][1000 genomes]
rs9401088	0.88[EUR][1000 genomes]
rs9481862	0.83[ASN][1000 genomes]
rs9481870	0.80[CHB][hapmap]
rs9481871	0.87[YRI][hapmap]
rs9489521	0.83[ASN][1000 genomes]
rs9489522	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9489523	0.91[ASN][1000 genomes]
rs9489526	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9489527	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9489531	0.81[ASN][1000 genomes]
rs9489535	0.80[CHB][hapmap];0.91[YRI][hapmap]
rs9489536	0.80[CHB][hapmap]
rs9489537	0.80[CHB][hapmap]
rs9489543	0.91[YRI][hapmap]
rs9489544	0.95[LWK][hapmap];0.91[YRI][hapmap]
rs9784804	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1025403	chr6:118635123-119122551	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1027444	chr6:118687556-119121660	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv538428	chr6:118687556-119121660	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv949321	chr6:118692304-119137658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv948980	chr6:118772508-119137658	Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv604559	chr6:118786486-119113317	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv830788	chr6:119014021-119143652	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1023826	chr6:119026481-119221408	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv886568	chr6:119044453-119132164	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv886569	chr6:119055873-119132164	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs962393	MCMDC1	cis	multi-tissue	Pritchard
rs962393	MCM9	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119095200-119105800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr6:119095600-119102000	Weak transcription	Placenta	Placenta
3	chr6:119098200-119104800	Weak transcription	Brain Anterior Caudate	brain
4	chr6:119098400-119104000	Weak transcription	Ovary	ovary
5	chr6:119098400-119104200	Weak transcription	Fetal Heart	heart
6	chr6:119098400-119104200	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:119098600-119104200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr6:119098600-119105000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:119098600-119105000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:119098600-119105600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:119098800-119101400	Weak transcription	Fetal Thymus	thymus
12	chr6:119098800-119102000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:119098800-119102200	Weak transcription	NHEK	skin
14	chr6:119098800-119104200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:119098800-119108800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:119099000-119102000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:119099000-119105800	Weak transcription	Pancreas	Pancrea
18	chr6:119099400-119101600	Weak transcription	HMEC	breast
19	chr6:119100200-119103200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr6:119101000-119102600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr6:119101000-119104800	Weak transcription	Fetal Brain Female	brain

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