Variant report

Variant	rs10912660
Chromosome Location	chr1:173637518-173637519
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10798295	0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs10912656	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10912676	0.82[ASN][1000 genomes]
rs12057778	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12065988	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12067170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12075071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12092383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12561820	0.95[CEU][hapmap]
rs4382766	0.82[CHB][hapmap]
rs4916362	0.82[CHB][hapmap]
rs57592568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674589	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6702835	0.87[CHB][hapmap]
rs727924	0.84[AMR][1000 genomes]
rs7314	0.87[CHB][hapmap]
rs7365380	0.89[ASN][1000 genomes]
rs7513933	0.83[AMR][1000 genomes]
rs7540065	0.87[CHB][hapmap]
rs7542910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7552939	0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs969029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9803671	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10912660		cis	Lymphoblastoid	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173625400-173638400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:173626000-173637600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:173630600-173646600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:173631000-173638600	Weak transcription	HMEC	breast
5	chr1:173632600-173638600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:173632600-173638600	Weak transcription	HSMM	muscle
7	chr1:173633600-173638200	Weak transcription	Right Atrium	heart
8	chr1:173636200-173638200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:173636200-173638600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:173636200-173638600	Weak transcription	Spleen	Spleen
11	chr1:173636600-173638400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:173636600-173638600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:173637200-173638000	Enhancers	Fetal Brain Female	brain
14	chr1:173637200-173638200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr1:173637400-173637600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:173637400-173637600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:173637400-173637600	Enhancers	H9 Cell Line	embryonic stem cell
18	chr1:173637400-173637600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:173637400-173637600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:173637400-173637600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:173637400-173637800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:173637400-173638200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:173637400-173638200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr1:173637400-173638400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:173637400-173639200	Active TSS	Brain Anterior Caudate	brain

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