Variant report

Variant	rs12725598
Chromosome Location	chr1:95093341-95093342
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:95092034..95094712-chr1:95098482..95100203,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11165186	0.85[ASN][1000 genomes]
rs11576456	0.87[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs11577320	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11580343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12401721	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12402912	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12725602	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726870	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2211318	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4847324	0.80[AMR][1000 genomes]
rs9645363	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12725598	GCLM	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95088800-95094200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr1:95089600-95095200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:95089800-95094200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:95089800-95100000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:95089800-95100400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:95090000-95102800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:95090200-95093600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:95090200-95094200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:95090200-95094200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:95090200-95094200	Weak transcription	NHEK	skin
11	chr1:95090200-95099600	Weak transcription	Fetal Stomach	stomach
12	chr1:95090600-95095000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:95090800-95100600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:95091000-95095000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:95091200-95094200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:95091600-95100400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:95092000-95093800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:95092400-95095000	Weak transcription	Right Ventricle	heart
19	chr1:95093200-95095800	Enhancers	Placenta Amnion	Placenta Amnion
20	chr1:95093200-95096000	Enhancers	Fetal Heart	heart
21	chr1:95093200-95096600	Enhancers	Placenta	Placenta

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