Variant report

Variant	rs3754409
Chromosome Location	chr1:226892377-226892378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226891369..226893117-chr1:226909879..226911474,2	MCF-7	breast:
2	chr1:226889377..226893057-chr1:226895503..226902234,11	MCF-7	breast:
3	chr1:226889403..226893513-chr1:226896039..226901883,9	MCF-7	breast:
4	chr1:226891869..226893550-chr1:226895150..226896872,2	K562	blood:
5	chr1:226884166..226888758-chr1:226889043..226894194,11	MCF-7	breast:
6	chr1:226862701..226865082-chr1:226889819..226892758,2	MCF-7	breast:
7	chr1:226891257..226894098-chr1:226898810..226900553,2	K562	blood:
8	chr1:226875941..226879287-chr1:226889966..226892608,3	MCF-7	breast:
9	chr1:226889929..226892747-chr1:227013300..227016016,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228382	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16846351	1.00[ASW][hapmap]
rs16846378	0.89[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs16846409	1.00[AMR][1000 genomes]
rs16846413	0.95[AMR][1000 genomes]
rs3754400	0.88[JPT][hapmap]
rs3754402	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3754406	0.89[JPT][hapmap]
rs3754407	1.00[ASW][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap]
rs3754413	1.00[ASW][hapmap]
rs3820641	0.89[JPT][hapmap]
rs41440951	1.00[ASW][hapmap];0.82[MEX][hapmap]
rs4653461	0.89[JPT][hapmap]
rs4653463	1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4653763	0.90[AMR][1000 genomes]
rs4653765	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4653766	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs60932168	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv997468	chr1:226858660-226975311	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv535316	chr1:226858660-226975311	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226886200-226895800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:226886200-226896000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:226891400-226892400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:226891400-226892400	Flanking Active TSS	Colon Smooth Muscle	Colon
5	chr1:226891400-226892800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr1:226891600-226892800	Enhancers	Brain Substantia Nigra	brain
7	chr1:226891600-226893400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:226891600-226893400	Weak transcription	Left Ventricle	heart
9	chr1:226891600-226893600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:226891600-226896000	Weak transcription	Esophagus	oesophagus
11	chr1:226891600-226896200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:226891600-226896200	Weak transcription	Spleen	Spleen
13	chr1:226891600-226896600	Weak transcription	Lung	lung
14	chr1:226891600-226898200	Weak transcription	Gastric	stomach
15	chr1:226891600-226899000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:226891600-226900600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:226891600-226900600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:226891600-226910200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:226891800-226892400	Enhancers	Primary B cells from peripheral blood	blood
20	chr1:226891800-226892400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:226891800-226892400	Enhancers	Brain Anterior Caudate	brain
22	chr1:226891800-226892400	Enhancers	Fetal Stomach	stomach
23	chr1:226891800-226892400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr1:226891800-226892600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr1:226891800-226892600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr1:226891800-226892600	Enhancers	Brain Angular Gyrus	brain
27	chr1:226891800-226892600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr1:226891800-226892600	Enhancers	Fetal Lung	lung
29	chr1:226891800-226892800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:226891800-226893000	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:226891800-226893000	Enhancers	Thymus	Thymus
32	chr1:226891800-226893200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:226891800-226893400	Weak transcription	Fetal Intestine Small	intestine
34	chr1:226891800-226893400	Weak transcription	Fetal Muscle Leg	muscle
35	chr1:226891800-226894000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:226891800-226894000	Weak transcription	Brain Germinal Matrix	brain
37	chr1:226891800-226894000	Weak transcription	HSMMtube	muscle
38	chr1:226891800-226894200	Weak transcription	Fetal Brain Male	brain
39	chr1:226891800-226894200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:226891800-226894400	Weak transcription	Psoas Muscle	Psoas
41	chr1:226891800-226894400	Weak transcription	Right Atrium	heart
42	chr1:226891800-226894400	Weak transcription	Right Ventricle	heart
43	chr1:226891800-226894400	Weak transcription	NHDF-Ad	bronchial
44	chr1:226891800-226894600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:226891800-226894800	Genic enhancers	Primary T cells fromperipheralblood	blood
46	chr1:226891800-226895200	Weak transcription	HUVEC	blood vessel
47	chr1:226891800-226895400	Weak transcription	Fetal Intestine Large	intestine
48	chr1:226891800-226895400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:226891800-226895400	Weak transcription	HMEC	breast
50	chr1:226891800-226895800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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