Variant report

Variant	rs12090953
Chromosome Location	chr1:172019555-172019556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172009534..172012040-chr1:172017929..172019999,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10752861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10911275	0.82[CEU][hapmap]
rs2761184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2761185	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2761186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2761187	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2761190	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2819531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28378748	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4244191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4641331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916418	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs6425637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425638	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6665598	1.00[CEU][hapmap];1.00[EUR][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	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	nsv3532	chr1:171997451-172042351	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3374464	chr1:172014139-172023467	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171994000-172020400	Weak transcription	Left Ventricle	heart
2	chr1:172006400-172025600	Weak transcription	Adipose Nuclei	Adipose
3	chr1:172009200-172022800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:172010000-172022200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:172010400-172022000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:172010600-172022400	Weak transcription	HMEC	breast
7	chr1:172010600-172051400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:172010800-172019800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:172010800-172022400	Weak transcription	NHEK	skin
10	chr1:172010800-172037600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:172011000-172019600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:172011400-172037800	Weak transcription	Ovary	ovary
13	chr1:172012600-172022600	Weak transcription	Fetal Lung	lung
14	chr1:172013000-172022400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:172014000-172023800	Weak transcription	Primary T cells from cord blood	blood
16	chr1:172014200-172024200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:172014600-172024400	Weak transcription	Brain Germinal Matrix	brain
18	chr1:172015000-172024200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:172015000-172033200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:172015000-172042600	Weak transcription	Fetal Brain Female	brain
21	chr1:172015200-172022800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:172015200-172026000	Weak transcription	Aorta	Aorta
23	chr1:172015200-172032400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:172016600-172037800	Weak transcription	Brain Substantia Nigra	brain
25	chr1:172017000-172022400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:172017800-172020200	Strong transcription	Brain Angular Gyrus	brain
27	chr1:172018200-172021400	Strong transcription	Brain Hippocampus Middle	brain
28	chr1:172018600-172021400	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr1:172019000-172020200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:172019000-172024200	Weak transcription	Brain Anterior Caudate	brain
31	chr1:172019400-172020000	Weak transcription	Brain Cingulate Gyrus	brain

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