Variant report

Variant	rs1408277
Chromosome Location	chr6:121811989-121811990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12201001	0.98[ASN][1000 genomes]
rs1359234	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1408278	0.93[ASN][1000 genomes]
rs1570630	0.82[ASN][1000 genomes]
rs2389547	0.95[ASN][1000 genomes]
rs4143301	0.82[ASN][1000 genomes]
rs4357173	0.82[ASN][1000 genomes]
rs4946571	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4946573	0.98[ASN][1000 genomes]
rs6569210	0.98[ASN][1000 genomes]
rs6569211	0.93[ASN][1000 genomes]
rs6569212	0.82[ASN][1000 genomes]
rs6901013	0.91[ASN][1000 genomes]
rs6921266	0.87[ASN][1000 genomes]
rs7742729	0.98[ASN][1000 genomes]
rs7748671	0.98[ASN][1000 genomes]
rs7762594	0.98[ASN][1000 genomes]
rs9387965	0.82[ASN][1000 genomes]
rs9398635	0.98[ASN][1000 genomes]
rs9401411	0.82[ASN][1000 genomes]
rs9490300	0.93[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	nsv5458	chr6:121787521-121823054	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1408277	KCTD21	trans	cerebellum	SCAN
rs1408277	HSF2	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:121807000-121812600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:121807400-121812600	Weak transcription	Hela-S3	cervix
3	chr6:121807400-121824400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:121809800-121812400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:121810000-121812600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:121810000-121812600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr6:121810000-121813000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:121810400-121812000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:121810400-121812400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:121810400-121812400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:121810600-121812400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:121810600-121812600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:121811000-121812600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:121811800-121812800	Enhancers	A549	lung
15	chr6:121811800-121813200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:121811800-121813200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr6:121811800-121813400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr6:121811800-121814000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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