Variant report

Variant	rs12088423
Chromosome Location	chr1:228380008-228380009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228373990..228375977-chr1:228378218..228380125,2	K562	blood:
2	chr1:228367725..228372821-chr1:228377689..228380181,6	MCF-7	breast:
3	chr1:228350293..228354874-chr1:228377436..228381142,4	MCF-7	breast:
4	chr1:228285041..228287250-chr1:228378476..228381097,2	MCF-7	breast:
5	chr1:228379718..228382551-chr1:228396432..228398212,3	K562	blood:
6	chr1:228349528..228352253-chr1:228378425..228381248,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181873	Chromatin interaction
ENSG00000203684	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10495278	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap]
rs10495279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11577976	1.00[CEU][hapmap]
rs11581037	1.00[CEU][hapmap]
rs11584418	1.00[CEU][hapmap]
rs11586055	1.00[CEU][hapmap]
rs3795774	1.00[CEU][hapmap]
rs4653906	1.00[CEU][hapmap]
rs6668719	1.00[CEU][hapmap]
rs7537552	1.00[CEU][hapmap]
rs9287011	1.00[CEU][hapmap]

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	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
2	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
3	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
4	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	91 gene(s)	inside rSNPs	diseases
6	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
7	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
8	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
10	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
11	esv1808523	chr1:228359177-228400358	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228354400-228384600	Weak transcription	Aorta	Aorta
2	chr1:228354600-228382200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:228354600-228385200	Weak transcription	Left Ventricle	heart
4	chr1:228363400-228386400	Weak transcription	Brain Angular Gyrus	brain
5	chr1:228363800-228385200	Weak transcription	Adipose Nuclei	Adipose
6	chr1:228364000-228384800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:228364400-228386600	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:228364400-228388600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:228364600-228386600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:228364800-228385600	Weak transcription	Brain Anterior Caudate	brain
11	chr1:228365000-228380400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:228365200-228386600	Weak transcription	Thymus	Thymus
13	chr1:228365200-228387800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:228365800-228382600	Weak transcription	Spleen	Spleen
15	chr1:228366000-228386400	Weak transcription	Primary B cells from cord blood	blood
16	chr1:228366800-228385200	Weak transcription	Ovary	ovary
17	chr1:228366800-228386600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:228366800-228393400	Weak transcription	Right Ventricle	heart
19	chr1:228371200-228386400	Weak transcription	Primary T cells from cord blood	blood
20	chr1:228373600-228382600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:228373800-228386200	Weak transcription	Fetal Stomach	stomach
22	chr1:228373800-228394000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:228376400-228382200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:228376400-228385200	Weak transcription	Fetal Brain Female	brain
25	chr1:228377800-228380800	Enhancers	Fetal Muscle Trunk	muscle
26	chr1:228379400-228380200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr1:228379400-228380400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr1:228379600-228380800	Enhancers	Fetal Muscle Leg	muscle
29	chr1:228379600-228380800	Enhancers	Lung	lung
30	chr1:228379600-228380800	Enhancers	Psoas Muscle	Psoas
31	chr1:228379800-228380200	Flanking Active TSS	K562	blood

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