Variant report

Variant	rs12564848
Chromosome Location	chr1:174276369-174276370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174269404..174272933-chr1:174275940..174280582,4	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10127823	0.82[EUR][1000 genomes]
rs12079820	0.80[CHB][hapmap]
rs12562344	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12564858	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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12564876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12565430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap]
rs12565675	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566643	0.90[CEU][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12567854	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12567864	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12568869	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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12691474	0.80[CHB][hapmap]
rs12737218	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1407126	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16828467	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16846667	0.82[EUR][1000 genomes]
rs16846688	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1890881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2015075	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41265242	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41266044	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4140468	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4442420	0.80[CHB][hapmap]
rs4652274	0.80[CHB][hapmap]
rs57651489	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58866024	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60005461	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60039606	0.82[EUR][1000 genomes]
rs61826863	1.00[AFR][1000 genomes]
rs61826865	1.00[AFR][1000 genomes]
rs61826867	1.00[AFR][1000 genomes]
rs61826868	1.00[AFR][1000 genomes]
rs61826869	1.00[AFR][1000 genomes]
rs61826873	1.00[AFR][1000 genomes]
rs61826876	0.87[AFR][1000 genomes]
rs61826877	0.87[AFR][1000 genomes]
rs61827889	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61827900	1.00[AFR][1000 genomes]
rs61827901	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs61827902	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs61827903	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs61827904	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs61827905	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs61828571	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61828574	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61828575	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61828576	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61828577	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61828578	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61828580	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61828583	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828584	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828587	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828589	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828590	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828591	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828592	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828595	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61828622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61828624	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61828625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61828627	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61828630	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61828631	1.00[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs61828635	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61828641	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61828645	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61828653	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7525325	0.85[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9970174	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv470746	chr1:174150850-174469905	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1001803	chr1:174176164-174367747	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1008993	chr1:174180019-174331358	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv872553	chr1:174195629-174373379	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv872554	chr1:174209978-174291950	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv1010069	chr1:174215293-174539512	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	esv1795045	chr1:174273004-174346276	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12564848	SERPINC1	cis	multi-tissue	Pritchard
rs12564848	SERPINC1	cis	Muscle Skeletal	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174242800-174277200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:174246200-174284200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:174259600-174277800	Weak transcription	K562	blood
4	chr1:174260400-174277200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:174270600-174279200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:174270800-174276600	Weak transcription	Esophagus	oesophagus
7	chr1:174270800-174276800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:174270800-174281400	Weak transcription	Right Ventricle	heart
9	chr1:174270800-174284200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:174270800-174285800	Weak transcription	Aorta	Aorta
11	chr1:174270800-174289800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:174271000-174276800	Weak transcription	Thymus	Thymus
13	chr1:174271000-174279400	Weak transcription	Fetal Stomach	stomach
14	chr1:174271000-174286400	Weak transcription	Spleen	Spleen
15	chr1:174271200-174277000	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:174271200-174277000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:174271200-174278600	Weak transcription	Placenta	Placenta
18	chr1:174271200-174285600	Weak transcription	Lung	lung
19	chr1:174271400-174276600	Weak transcription	Brain Substantia Nigra	brain
20	chr1:174272200-174278000	Weak transcription	NHDF-Ad	bronchial
21	chr1:174272600-174283200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:174273000-174276400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr1:174273200-174288800	Weak transcription	Small Intestine	intestine
24	chr1:174273400-174277000	Weak transcription	Brain Angular Gyrus	brain
25	chr1:174274000-174276600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:174274000-174277000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:174274000-174277200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:174274000-174278400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:174274200-174276800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:174274400-174276400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:174274600-174276800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:174274600-174278800	Weak transcription	Fetal Heart	heart
33	chr1:174274800-174276600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:174274800-174277600	Weak transcription	Fetal Intestine Large	intestine
35	chr1:174274800-174279600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:174274800-174285800	Weak transcription	Left Ventricle	heart
37	chr1:174274800-174286000	Weak transcription	Pancreas	Pancrea
38	chr1:174275200-174279200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:174275600-174276600	Strong transcription	Liver	Liver
40	chr1:174275600-174276800	Strong transcription	Primary B cells from cord blood	blood
41	chr1:174275600-174276800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:174275600-174278200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:174275600-174279200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:174275600-174287600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:174275800-174276400	Strong transcription	Ovary	ovary
46	chr1:174275800-174276600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:174275800-174277000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:174275800-174277200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr1:174275800-174277800	ZNF genes & repeats	GM12878-XiMat	blood
50	chr1:174275800-174278400	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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