Variant report

Variant	rs693370
Chromosome Location	chr9:22446297-22446298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr9:22446278-22448068	A549	lung:	n/a	n/a
2	E2F6	chr9:22446232-22446981	A549	lung:	n/a	chr9:22446688-22446697

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:22402119..22404171-chr9:22444827..22446805,2	MCF-7	breast:

Variant related genes	Relation type
DMRTA1	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2671621	0.89[AFR][1000 genomes]
rs2671622	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34254072	0.81[EUR][1000 genomes]
rs534632	1.00[ASN][1000 genomes]
rs560612	1.00[ASN][1000 genomes]
rs585376	1.00[ASN][1000 genomes]
rs6475646	0.96[ASN][1000 genomes]
rs666258	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1029289	chr9:22193167-23023688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1031822	chr9:22364573-22490686	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv869121	chr9:22382290-23232146	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv892750	chr9:22383816-22496640	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv2761508	chr9:22400968-22819938	Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1016983	chr9:22412948-22672062	Bivalent/Poised TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1027227	chr9:22416348-22666768	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv540088	chr9:22416348-22666768	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv533941	chr9:22416549-23232146	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs693370	BMPR1A	trans	lymphoblastoid	seeQTL
rs693370	DMRTA1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22445000-22446400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:22446000-22450400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:22446200-22446400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr9:22446200-22446400	Enhancers	H1 Cell Line	embryonic stem cell
5	chr9:22446200-22446400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:22446200-22446400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:22446200-22446400	Enhancers	Adipose Nuclei	Adipose
8	chr9:22446200-22446400	Enhancers	Liver	Liver
9	chr9:22446200-22446400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr9:22446200-22446400	Enhancers	Fetal Kidney	kidney
11	chr9:22446200-22446400	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr9:22446200-22446400	Enhancers	Hela-S3	cervix
13	chr9:22446200-22446400	Enhancers	HUVEC	blood vessel
14	chr9:22446200-22446600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr9:22446200-22446600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr9:22446200-22446600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
17	chr9:22446200-22446600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr9:22446200-22446600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:22446200-22446600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:22446200-22446600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr9:22446200-22446600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr9:22446200-22446600	Flanking Active TSS	A549	lung
23	chr9:22446200-22446800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:22446200-22447000	Active TSS	Stomach Smooth Muscle	stomach
25	chr9:22446200-22447600	Active TSS	NH-A	brain
26	chr9:22446200-22447800	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr9:22446200-22447800	Active TSS	Aorta	Aorta
28	chr9:22446200-22447800	Active TSS	Colon Smooth Muscle	Colon
29	chr9:22446200-22449000	Active TSS	Brain Anterior Caudate	brain
30	chr9:22446200-22449200	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr9:22446200-22449600	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr9:22446200-22450000	Active TSS	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links