Variant report

Variant	rs2535240
Chromosome Location	chr6:29643877-29643878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs2535238	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2747421	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2747427	0.85[EUR][1000 genomes]
rs2747428	0.85[EUR][1000 genomes]
rs2747429	0.85[EUR][1000 genomes]
rs2747431	0.80[AFR][1000 genomes]
rs2747457	0.82[AFR][1000 genomes]
rs3129062	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs374317	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs375248	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs375984	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs376319	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs387640	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs387642	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs416568	0.83[AFR][1000 genomes]
rs417764	0.85[EUR][1000 genomes]
rs448380	0.83[EUR][1000 genomes]
rs448489	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2535240	C6orf12	Cis_1M	lymphoblastoid	RTeQTL
rs2535240	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2535240	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs2535240	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29636600-29644800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:29637000-29644400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:29638800-29644400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:29639600-29647400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:29643000-29646400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:29643000-29648800	Enhancers	HMEC	breast
8	chr6:29643200-29648400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:29643400-29648400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:29643600-29644600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:29643800-29644400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr6:29643800-29644600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:29643800-29644800	Enhancers	NHEK	skin
14	chr6:29643800-29647600	Enhancers	Fetal Heart	heart

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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