Variant report

Variant	rs1968688
Chromosome Location	chr15:58822747-58822748
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12898984	1.00[YRI][hapmap]
rs12900448	1.00[YRI][hapmap]
rs1823697	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1823698	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1839929	1.00[YRI][hapmap]
rs1968690	1.00[YRI][hapmap]
rs2034613	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2414580	1.00[AMR][1000 genomes]
rs261340	1.00[AMR][1000 genomes]
rs2899631	1.00[YRI][hapmap]
rs4503731	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4775068	1.00[YRI][hapmap]
rs504846	1.00[AMR][1000 genomes]
rs7165736	1.00[AMR][1000 genomes]
rs7167672	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7180936	1.00[YRI][hapmap]
rs73420505	1.00[AMR][1000 genomes]
rs8029789	1.00[AMR][1000 genomes]
rs8037479	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv569601	chr15:58800766-58866156	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv524098	chr15:58820978-58834391	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1968688	HBD	trans	lymphoblastoid	seeQTL
rs1968688	STK17B	trans	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58818000-58825200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr15:58820200-58823400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:58820400-58824000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:58821000-58826400	Weak transcription	Colonic Mucosa	Colon
5	chr15:58821000-58827400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr15:58821200-58823200	Enhancers	Liver	Liver
7	chr15:58821200-58824400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:58821200-58824400	Weak transcription	Gastric	stomach
9	chr15:58821200-58832200	Weak transcription	Fetal Kidney	kidney
10	chr15:58821400-58826200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:58821600-58824800	Weak transcription	Stomach Mucosa	stomach
12	chr15:58821600-58825000	Weak transcription	A549	lung
13	chr15:58821600-58838000	Weak transcription	Right Atrium	heart
14	chr15:58822200-58823200	Weak transcription	Spleen	Spleen
15	chr15:58822400-58827200	Weak transcription	HepG2	liver
16	chr15:58822600-58827600	Weak transcription	Pancreas	Pancrea

Quick Search:

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

what's new

Quick links