Variant report

Variant	rs1819871
Chromosome Location	chr12:12378065-12378066
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12373050..12374895-chr12:12377294..12378845,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10492120	0.90[CHB][hapmap]
rs10743980	0.90[CHB][hapmap]
rs10772536	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10772537	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10772540	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10772542	0.89[CHB][hapmap]
rs10772547	0.90[CHB][hapmap]
rs10845489	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10845491	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10845492	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10845494	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10845495	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10845501	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11054718	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11054721	1.00[CHB][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11054724	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11054731	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11054744	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11054754	0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs11609634	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12366664	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12823243	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17819999	1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2302684	0.81[AMR][1000 genomes]
rs2417085	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2417086	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3782528	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4477532	0.81[AMR][1000 genomes]
rs4763785	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61920859	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6488507	0.85[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7294695	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7302808	0.83[EUR][1000 genomes]
rs7305037	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7956548	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7956971	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7966410	1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7973531	0.90[CHB][hapmap]
rs7979447	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
2	chr12:12368200-12379000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:12368200-12381400	Weak transcription	Gastric	stomach
4	chr12:12368200-12384200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:12368600-12381000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:12368600-12381400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:12370600-12380800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:12370600-12381000	Weak transcription	Left Ventricle	heart
10	chr12:12370800-12379000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:12370800-12380800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:12370800-12392200	Weak transcription	Brain Substantia Nigra	brain
13	chr12:12371800-12378200	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:12373000-12380800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:12373000-12381200	Weak transcription	Lung	lung
16	chr12:12374600-12381000	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:12374600-12381400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:12374800-12380600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:12374800-12380600	Weak transcription	Brain Angular Gyrus	brain
20	chr12:12374800-12380800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:12374800-12383200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:12375000-12378200	Weak transcription	Fetal Intestine Large	intestine
23	chr12:12375000-12379200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:12375000-12380800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:12375200-12379200	Weak transcription	Liver	Liver
26	chr12:12375200-12379400	Weak transcription	Fetal Kidney	kidney
27	chr12:12375800-12379000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:12376200-12378400	Enhancers	GM12878-XiMat	blood
29	chr12:12376600-12378200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:12376800-12378400	Enhancers	NHLF	lung
31	chr12:12376800-12380000	Enhancers	HepG2	liver
32	chr12:12377200-12378800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:12377200-12378800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:12377200-12381000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:12377200-12381200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:12377400-12382400	Weak transcription	HSMM	muscle
37	chr12:12377800-12378200	ZNF genes & repeats	Fetal Stomach	stomach
38	chr12:12377800-12378800	Weak transcription	A549	lung
39	chr12:12377800-12384200	Weak transcription	K562	blood
40	chr12:12377800-12407200	Weak transcription	NH-A	brain
41	chr12:12378000-12378200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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