Variant report

Variant	rs12075554
Chromosome Location	chr1:9767817-9767818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:9767627-9767847	HepG2	liver:	n/a	chr1:9767780-9767791
2	CEBPB	chr1:9767663-9767838	A549	lung:	n/a	chr1:9767780-9767791
3	CEBPB	chr1:9767617-9767873	IMR90	lung:	n/a	chr1:9767780-9767791
4	CEBPB	chr1:9767617-9767938	K562	blood:	n/a	chr1:9767780-9767791
5	CEBPB	chr1:9767678-9767820	Hela-S3	cervix:	n/a	chr1:9767780-9767791

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9766560..9769442-chr1:9772141..9775088,2	K562	blood:

Variant related genes	Relation type
PIK3CD	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10779731	0.85[MEX][hapmap]
rs10864435	1.00[CEU][hapmap]
rs11121480	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11121484	1.00[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes]
rs12028908	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12047054	0.90[MEX][hapmap]
rs12566637	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12568720	0.89[MEX][hapmap]
rs12569008	0.90[MEX][hapmap]
rs3934934	0.92[CEU][hapmap];0.90[MEX][hapmap]
rs72633866	0.84[AMR][1000 genomes]
rs7526958	0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv3424708	chr1:9748735-9771466	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12075554	THAP3	cis	cerebellum	SCAN
rs12075554	TNFRSF1B	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9750400-9770400	Weak transcription	Brain Substantia Nigra	brain
2	chr1:9750600-9775800	Weak transcription	Pancreas	Pancrea
3	chr1:9750600-9813000	Weak transcription	Right Atrium	heart
4	chr1:9750800-9770000	Weak transcription	Adipose Nuclei	Adipose
5	chr1:9750800-9770000	Weak transcription	Aorta	Aorta
6	chr1:9750800-9771600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:9750800-9775400	Weak transcription	Gastric	stomach
8	chr1:9751000-9770200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:9751000-9770400	Weak transcription	Fetal Brain Female	brain
10	chr1:9751000-9775600	Weak transcription	Esophagus	oesophagus
11	chr1:9751000-9777600	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:9751000-9779800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:9752000-9774000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:9752400-9776000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:9754800-9771200	Weak transcription	Ovary	ovary
16	chr1:9761000-9773200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:9761000-9779000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:9761000-9781600	Weak transcription	HSMMtube	muscle
19	chr1:9761200-9770400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:9761200-9773400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:9761200-9774400	Weak transcription	Lung	lung
22	chr1:9761200-9775600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:9761400-9774000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:9761400-9774000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:9761400-9777200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:9761400-9778000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:9761800-9769800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:9763200-9782400	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:9763800-9768000	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr1:9764000-9774600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:9764400-9770000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:9764400-9770200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:9764600-9770000	Weak transcription	Fetal Intestine Small	intestine
34	chr1:9764600-9770200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:9764600-9777000	Weak transcription	Liver	Liver
36	chr1:9765000-9770200	Weak transcription	Spleen	Spleen
37	chr1:9765000-9776400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:9765400-9770000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:9765400-9770200	Weak transcription	Thymus	Thymus
40	chr1:9765400-9770400	Weak transcription	Fetal Thymus	thymus
41	chr1:9765400-9776400	Weak transcription	Placenta	Placenta
42	chr1:9765600-9768600	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr1:9765600-9769600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr1:9765600-9769600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:9765600-9770000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:9765600-9770000	Weak transcription	GM12878-XiMat	blood
47	chr1:9765600-9770200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:9765600-9772000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:9765800-9773200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:9766000-9768400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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