Variant report

Variant	rs12401893
Chromosome Location	chr1:228196321-228196322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228190036..228193608-chr1:228195528..228197492,3	MCF-7	breast:
2	chr1:228194854..228196535-chr1:228199538..228201142,2	MCF-7	breast:
3	chr1:228191215..228193545-chr1:228195515..228198090,2	MCF-7	breast:
4	chr1:228194958..228197764-chr1:228296157..228297740,2	K562	blood:
5	chr1:228193720..228196616-chr1:228296879..228298469,2	MCF-7	breast:
6	chr1:228195432..228198403-chr1:228200183..228201767,2	K562	blood:
7	chr1:228192379..228197446-chr1:228268248..228273367,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162910	Chromatin interaction
ENSG00000143761	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1323023	0.87[ASN][1000 genomes]
rs4066662	0.87[ASN][1000 genomes]
rs60356098	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv947387	chr1:228140028-228206630	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
10	nsv945349	chr1:228186556-228245135	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv826953	chr1:228191929-228196867	Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228192200-228196800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:228193400-228196600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:228193800-228196800	Enhancers	Primary B cells from cord blood	blood
4	chr1:228194000-228196600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
5	chr1:228194200-228196600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr1:228194200-228197400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr1:228194800-228197200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr1:228195000-228196600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
9	chr1:228195000-228196800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr1:228195200-228197200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:228195200-228197200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:228195200-228197200	Bivalent Enhancer	Spleen	Spleen
13	chr1:228195200-228213200	Weak transcription	Right Atrium	heart
14	chr1:228195400-228196600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
15	chr1:228195600-228196600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:228195600-228196800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:228195600-228197200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:228195800-228196400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:228195800-228197200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:228196000-228196400	Bivalent Enhancer	Placenta	Placenta
21	chr1:228196000-228197000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
22	chr1:228196200-228196400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
23	chr1:228196200-228196400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:228196200-228196400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
25	chr1:228196200-228196400	Bivalent Enhancer	Fetal Brain Female	brain
26	chr1:228196200-228196600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:228196200-228196800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
28	chr1:228196200-228197400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links