Variant report

Variant	rs1144838
Chromosome Location	chr1:226821306-226821307
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226820706..226823635-chr1:226824832..226827182,2	MCF-7	breast:
2	chr1:226820120..226821786-chr1:226825137..226827327,2	K562	blood:
3	chr1:226821201..226822498-chr1:227015438..227016431,9	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10495246	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1144839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151804	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1288936	0.85[JPT][hapmap]
rs17522524	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17588687	0.90[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3768376	0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs3820635	0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3820637	0.90[CHB][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes]
rs697843	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7533764	0.84[EUR][1000 genomes]

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	nsv470779	chr1:226778432-226833304	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv873234	chr1:226779449-226859676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv873235	chr1:226819073-226851963	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	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
rs1144838	CABC1	cis	cerebellum	SCAN
rs1144838	PARP1	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226806200-226825800	Weak transcription	Right Atrium	heart
2	chr1:226810600-226822600	Weak transcription	Gastric	stomach
3	chr1:226814200-226821400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:226814200-226823600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:226814200-226837600	Weak transcription	HUVEC	blood vessel
6	chr1:226814400-226821600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:226814600-226824200	Weak transcription	Brain Angular Gyrus	brain
8	chr1:226814600-226824800	Weak transcription	Liver	Liver
9	chr1:226814800-226821600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:226814800-226830400	Strong transcription	Thymus	Thymus
11	chr1:226814800-226834800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:226814800-226840600	Weak transcription	Small Intestine	intestine
13	chr1:226815000-226821600	Weak transcription	Esophagus	oesophagus
14	chr1:226815000-226823800	Weak transcription	Ovary	ovary
15	chr1:226815200-226821400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:226816800-226837000	Weak transcription	Fetal Brain Male	brain
17	chr1:226817000-226837000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:226817200-226825400	Strong transcription	Lung	lung
19	chr1:226817200-226828000	Weak transcription	Fetal Brain Female	brain
20	chr1:226817200-226830600	Strong transcription	Fetal Intestine Small	intestine
21	chr1:226817600-226821400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:226817800-226821400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:226817800-226822800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:226817800-226828000	Weak transcription	Aorta	Aorta
25	chr1:226818000-226824400	Weak transcription	Fetal Lung	lung
26	chr1:226818200-226826400	Weak transcription	Pancreas	Pancrea
27	chr1:226818400-226821600	Weak transcription	NHLF	lung
28	chr1:226818600-226822400	Genic enhancers	Fetal Stomach	stomach
29	chr1:226818600-226823400	Enhancers	Primary B cells from cord blood	blood
30	chr1:226818600-226823400	Genic enhancers	Stomach Smooth Muscle	stomach
31	chr1:226818600-226825200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:226819000-226822200	Enhancers	Primary B cells from peripheral blood	blood
33	chr1:226819200-226821600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr1:226819200-226822400	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr1:226819200-226822800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:226819200-226825200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr1:226819200-226830200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:226819400-226821600	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr1:226819400-226823200	Genic enhancers	Brain Hippocampus Middle	brain
40	chr1:226819600-226826600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:226819800-226821400	Genic enhancers	GM12878-XiMat	blood
42	chr1:226819800-226821800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:226819800-226822000	Enhancers	Brain Germinal Matrix	brain
44	chr1:226819800-226823000	Genic enhancers	Fetal Muscle Leg	muscle
45	chr1:226819800-226823200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:226819800-226824000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:226819800-226825400	Genic enhancers	Spleen	Spleen
48	chr1:226820000-226821400	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:226820000-226821600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:226820000-226822000	Genic enhancers	Brain Inferior Temporal Lobe	brain

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