Variant report

Variant	rs35029375
Chromosome Location	chr1:227054200-227054201
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	SETDB1	chr1:227054108-227054349	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227051915..227054203-chr1:227056473..227058361,2	K562	blood:

Variant related genes	Relation type
PSEN2	TF binding region
ENSG00000143801	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10799367	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10916057	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916059	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11580744	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11588886	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12119853	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12123818	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12125811	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12127440	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12130732	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12138310	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12143886	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12403248	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12405779	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12733650	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12747261	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12760155	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16846644	0.95[EUR][1000 genomes]
rs1800672	0.97[EUR][1000 genomes]
rs1800673	0.97[EUR][1000 genomes]
rs1800681	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236912	0.94[EUR][1000 genomes]
rs3213436	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34081886	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35213802	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35244407	0.82[EUR][1000 genomes]
rs35396772	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35519961	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35744376	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3820649	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3829979	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6426554	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6676065	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6676067	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6680780	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71648404	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs732479	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7512804	0.93[EUR][1000 genomes];0.89[ASN][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	nsv4766	chr1:227025954-227070961	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3381082	chr1:227029266-227059927	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
4	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227045200-227057800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:227051600-227054200	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr1:227051600-227055200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:227051600-227057800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:227051600-227057800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:227051600-227057800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:227051800-227054800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:227051800-227055200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:227051800-227055400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:227051800-227057800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:227051800-227057800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:227051800-227057800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:227051800-227057800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:227051800-227057800	Weak transcription	Osteobl	bone
15	chr1:227052000-227054600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:227052000-227054800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:227052000-227055200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:227052000-227057800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:227052200-227054800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:227052200-227057800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:227052400-227057800	Weak transcription	Pancreas	Pancrea
22	chr1:227053000-227057800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:227053400-227054200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:227053400-227054200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr1:227053400-227054600	Enhancers	HMEC	breast
26	chr1:227053400-227055600	Enhancers	NHEK	skin
27	chr1:227053400-227057800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:227053600-227054400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr1:227053600-227054400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:227053600-227055200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:227053600-227057600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:227053600-227057800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:227053600-227057800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr1:227053800-227055200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr1:227053800-227055200	Weak transcription	Hela-S3	cervix
36	chr1:227053800-227055400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:227053800-227057800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:227053800-227057800	Weak transcription	Liver	Liver
39	chr1:227053800-227057800	Weak transcription	NHDF-Ad	bronchial
40	chr1:227053800-227057800	Weak transcription	NHLF	lung
41	chr1:227053800-227058000	Weak transcription	Gastric	stomach
42	chr1:227054000-227054200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:227054200-227057800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:227054200-227057800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:227054200-227057800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:227054200-227057800	Weak transcription	Rectal Mucosa Donor 31	rectum

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