Variant report

Variant	rs1281425
Chromosome Location	chr1:179802903-179802904
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179785943..179788290-chr1:179801388..179803058,2	K562	blood:
2	chr1:179795002..179797734-chr1:179802507..179804138,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229407	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1148813	0.91[ASN][1000 genomes]
rs1148814	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[ASN][1000 genomes]
rs1148816	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1148818	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148819	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs1281409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1281414	0.84[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1281415	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs1281419	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1281424	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1281431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1290274	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1295972	1.00[ASN][1000 genomes]
rs1299683	1.00[ASN][1000 genomes]
rs1299685	0.91[ASN][1000 genomes]
rs17370666	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1758143	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2777916	1.00[ASN][1000 genomes]
rs2794584	0.83[ASN][1000 genomes]
rs524166	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs576723	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs627897	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap]
rs651455	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs668813	1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs872376	0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1281425	FAM163A	cis	parietal	SCAN
rs1281425	SOAT1	cis	multi-tissue	Pritchard
rs1281425	TNN	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179791000-179807200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:179793800-179808800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr1:179794600-179804800	Weak transcription	Right Ventricle	heart
4	chr1:179794800-179809200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:179795200-179812400	Weak transcription	Left Ventricle	heart
6	chr1:179795200-179815200	Weak transcription	Ovary	ovary
7	chr1:179795400-179804600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:179795400-179804800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:179795400-179805000	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:179795400-179807600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:179795400-179815200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:179795600-179834200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:179797400-179805800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr1:179797600-179810000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:179798400-179805800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:179799600-179815200	Weak transcription	Brain Angular Gyrus	brain
17	chr1:179799800-179804800	Weak transcription	Adipose Nuclei	Adipose
18	chr1:179800400-179808800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:179800400-179809000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:179800400-179815200	Weak transcription	Psoas Muscle	Psoas
21	chr1:179800600-179815200	Weak transcription	Esophagus	oesophagus
22	chr1:179800800-179808800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:179800800-179815200	Weak transcription	Hela-S3	cervix
24	chr1:179801000-179805000	Weak transcription	Aorta	Aorta
25	chr1:179801000-179814400	Weak transcription	HMEC	breast
26	chr1:179801000-179815000	Weak transcription	K562	blood
27	chr1:179801200-179804800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:179801200-179804800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:179801200-179808800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:179801200-179809400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:179801200-179810400	Weak transcription	HSMMtube	muscle
32	chr1:179801200-179815200	Weak transcription	Lung	lung
33	chr1:179801200-179815200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:179801200-179815200	Weak transcription	Spleen	Spleen
35	chr1:179801400-179808000	Weak transcription	Pancreas	Pancrea
36	chr1:179801400-179810200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:179801400-179810600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:179801400-179810600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:179801600-179813200	Weak transcription	GM12878-XiMat	blood
40	chr1:179801800-179807200	Weak transcription	Osteobl	bone
41	chr1:179801800-179808600	Weak transcription	Liver	Liver
42	chr1:179801800-179808600	Weak transcription	HSMM	muscle
43	chr1:179801800-179808800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:179801800-179813200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:179801800-179815200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:179801800-179815200	Weak transcription	NHDF-Ad	bronchial
47	chr1:179802200-179804000	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr1:179802200-179804400	Weak transcription	Fetal Intestine Small	intestine
49	chr1:179802200-179804800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:179802200-179815200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links