Variant report

Variant	rs12409869
Chromosome Location	chr1:59201426-59201427
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	chr1:59200101..59201638-chr1:59243115..59244926,2	K562	blood:
2	chr1:59200565..59206514-chr1:59243497..59250904,12	K562	blood:

Variant related genes	Relation type
ENSG00000234807	Chromatin interaction
ENSG00000177606	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10889115	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583201	0.92[CEU][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12118682	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143680	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12405774	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17117956	0.83[CEU][hapmap];0.92[JPT][hapmap]
rs17118103	0.92[JPT][hapmap]
rs17118106	0.92[JPT][hapmap]
rs232777	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs232780	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs232782	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs232786	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs232787	0.82[CEU][hapmap]
rs232794	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs232795	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs232853	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs232855	0.85[CEU][hapmap]
rs232860	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs232871	0.85[CEU][hapmap];0.91[JPT][hapmap]
rs232874	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs232876	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs232882	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs232885	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs232892	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs232894	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs232895	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs34882065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587835	0.85[CEU][hapmap];0.92[JPT][hapmap]
rs7524931	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528508	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7548025	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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	esv2754829	chr1:59197556-59215791	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12409869	MYSM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59192600-59204200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr1:59198200-59206200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:59198600-59205800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:59198800-59204000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:59198800-59207200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:59200400-59205800	Weak transcription	NHDF-Ad	bronchial
7	chr1:59201000-59204000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:59201200-59201800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:59201400-59202000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:59201400-59202600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:59201400-59203200	Enhancers	Dnd41	blood

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