Variant report

Variant	rs2849397
Chromosome Location	chr18:12044082-12044083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12038572..12040680-chr18:12043555..12046070,2	MCF-7	breast:
2	chr18:12035639..12037274-chr18:12041657..12044195,2	MCF-7	breast:
3	chr18:11907841..11909998-chr18:12042409..12044684,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266995	Chromatin interaction
ENSG00000273141	Chromatin interaction
ENSG00000154889	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12458258	0.81[EUR][1000 genomes]
rs12970359	0.91[EUR][1000 genomes]
rs1662608	0.91[ASN][1000 genomes]
rs1787982	0.90[ASN][1000 genomes]
rs1815926	0.83[EUR][1000 genomes]
rs1962196	0.81[CEU][hapmap]
rs2012779	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2165855	0.91[ASN][1000 genomes]
rs2849394	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2849395	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2849396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2849398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2849399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851912	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851913	0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2851914	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2851918	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34203217	0.89[EUR][1000 genomes]
rs35815920	0.85[EUR][1000 genomes]
rs3923383	0.80[CEU][hapmap]
rs4291976	0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4386188	0.81[CEU][hapmap]
rs4580259	0.91[ASN][1000 genomes]
rs4580260	1.00[JPT][hapmap]
rs4797608	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4797609	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4797610	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4797611	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs582959	0.87[ASN][1000 genomes]
rs591447	0.91[ASN][1000 genomes]
rs622443	0.81[ASN][1000 genomes]
rs627965	0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs630110	0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs639876	0.91[ASN][1000 genomes]
rs639966	0.91[ASN][1000 genomes]
rs640340	0.91[ASN][1000 genomes]
rs642585	0.91[ASN][1000 genomes]
rs6505709	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655651	0.91[ASN][1000 genomes]
rs657476	0.91[ASN][1000 genomes]
rs7238163	0.81[CEU][hapmap]
rs8083502	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8090265	0.92[ASN][1000 genomes]
rs9945059	0.81[CEU][hapmap]
rs9953936	0.81[CEU][hapmap]
rs9955653	0.81[CEU][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv909393	chr18:12001258-12155371	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv909394	chr18:12017343-12141372	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv978603	chr18:12039958-12046831	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2849397	MC5R	cis	parietal	SCAN
rs2849397	KIAA0802	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12039400-12044800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr18:12039400-12045800	Weak transcription	Pancreas	Pancrea
3	chr18:12039400-12047000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr18:12039400-12047400	Weak transcription	Gastric	stomach
5	chr18:12039400-12048400	Weak transcription	Right Ventricle	heart
6	chr18:12042000-12044400	Weak transcription	NH-A	brain
7	chr18:12042000-12048600	Weak transcription	HSMMtube	muscle
8	chr18:12042400-12044400	Weak transcription	Osteobl	bone
9	chr18:12042400-12045200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr18:12042400-12045400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr18:12042400-12045600	Weak transcription	HMEC	breast
12	chr18:12042800-12045600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr18:12042800-12048200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr18:12043000-12045400	Weak transcription	GM12878-XiMat	blood
15	chr18:12043600-12044400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr18:12043800-12044400	Flanking Bivalent TSS/Enh	HepG2	liver
17	chr18:12044000-12046200	Weak transcription	Lung	lung

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