Variant report

Variant	rs12738550
Chromosome Location	chr1:95090677-95090678
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:95087249..95089894-chr1:95090024..95092198,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235565	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12132926	0.90[ASN][1000 genomes]
rs1245481	0.85[CHD][hapmap]
rs12724134	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1361868	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17403082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17411251	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17411335	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17411572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35415294	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3814015	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847206	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4847316	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4847321	1.00[ASN][1000 genomes]
rs4847322	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55923008	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66472521	1.00[ASN][1000 genomes]
rs6694645	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72729587	0.89[AFR][1000 genomes];1.00[ASN][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	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv519997	chr1:95083836-95113417	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1001230	chr1:95085184-95108531	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr1:95085200-95090800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:95086600-95091200	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr1:95087800-95091000	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr1:95088000-95092000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:95088200-95091000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr1:95088200-95091200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr1:95088200-95091600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr1:95088800-95091600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr1:95088800-95094200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:95089200-95091200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr1:95089200-95091400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr1:95089600-95095200	Weak transcription	Fetal Intestine Small	intestine
13	chr1:95089800-95093200	Weak transcription	Fetal Heart	heart
14	chr1:95089800-95094200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:95089800-95100000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:95089800-95100400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:95090000-95102800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:95090200-95093600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:95090200-95094200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:95090200-95094200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:95090200-95094200	Weak transcription	NHEK	skin
22	chr1:95090200-95099600	Weak transcription	Fetal Stomach	stomach
23	chr1:95090400-95090800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:95090600-95091000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr1:95090600-95091200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:95090600-95093200	Weak transcription	Placenta	Placenta
27	chr1:95090600-95093200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:95090600-95095000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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