Variant report

Variant	rs12249697
Chromosome Location	chr10:99030478-99030479
allele	A/G
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	FOXA1	chr10:99030236-99030616	HepG2	liver:	n/a	n/a
2	KAP1	chr10:99030220-99030963	K562	blood:	n/a	n/a
3	SETDB1	chr10:99030453-99030862	U2OS	brain:	n/a	n/a
4	TEAD4	chr10:99030362-99030757	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:99028447..99031711-chr10:99092744..99094330,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231398	TF binding region
ARHGAP19	TF binding region
ENSG00000225850	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10466168	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11189044	1.00[ASW][hapmap];0.95[MKK][hapmap]
rs11189045	1.00[ASW][hapmap];0.92[MKK][hapmap];0.87[YRI][hapmap]
rs11189088	1.00[AMR][1000 genomes]
rs11189101	1.00[AMR][1000 genomes]
rs11189105	1.00[AMR][1000 genomes]
rs11189108	1.00[AMR][1000 genomes]
rs11189219	1.00[CHD][hapmap]
rs12244658	1.00[ASW][hapmap];0.83[MKK][hapmap]
rs12254370	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs12261079	1.00[AMR][1000 genomes]
rs12263021	1.00[AMR][1000 genomes]
rs12360068	1.00[CHD][hapmap]
rs12573086	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1041614	chr10:98928281-99083056	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1045553	chr10:98944397-99122203	Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv540750	chr10:98944397-99122203	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
5	esv1797410	chr10:98983785-99041740	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1040903	chr10:98986382-99047475	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv831952	chr10:98998344-99145924	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv895914	chr10:99006083-99131676	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12249697	PXDN	trans	lymphoblastoid	seeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98978600-99037400	Weak transcription	HSMM	muscle
2	chr10:98978600-99051800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:98983000-99037600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr10:98984600-99037600	Weak transcription	Brain Hippocampus Middle	brain
5	chr10:98987200-99051200	Weak transcription	Pancreas	Pancrea
6	chr10:98989000-99034600	Weak transcription	Aorta	Aorta
7	chr10:98989600-99038000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr10:98990000-99034600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr10:98994600-99039000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:99004800-99037400	Weak transcription	Fetal Heart	heart
11	chr10:99005200-99046800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr10:99013200-99037600	Weak transcription	NHLF	lung
13	chr10:99015000-99038000	Weak transcription	Fetal Brain Male	brain
14	chr10:99015400-99038200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr10:99016000-99038600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr10:99016200-99038200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:99016800-99038600	Weak transcription	HUVEC	blood vessel
18	chr10:99019200-99034600	Weak transcription	Liver	Liver
19	chr10:99019400-99038200	Weak transcription	K562	blood
20	chr10:99019400-99050000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr10:99019400-99051600	Weak transcription	Ovary	ovary
22	chr10:99021400-99051000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr10:99023600-99051200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr10:99024000-99034400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr10:99024000-99046800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr10:99024000-99050800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr10:99024400-99050000	Weak transcription	Spleen	Spleen
28	chr10:99024800-99034600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr10:99024800-99051200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr10:99025600-99034600	Weak transcription	Primary B cells from peripheral blood	blood
31	chr10:99025800-99037200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr10:99025800-99037400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr10:99025800-99038000	Weak transcription	Fetal Stomach	stomach
34	chr10:99025800-99039200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr10:99025800-99039200	Weak transcription	Fetal Muscle Leg	muscle
36	chr10:99025800-99050800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:99026000-99037400	Weak transcription	Dnd41	blood
38	chr10:99026000-99037400	Weak transcription	GM12878-XiMat	blood
39	chr10:99026000-99038600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr10:99026000-99051200	Weak transcription	Primary T cells from cord blood	blood
41	chr10:99026200-99037400	Weak transcription	Primary B cells from cord blood	blood
42	chr10:99026200-99037400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr10:99027600-99046200	Weak transcription	Thymus	Thymus
44	chr10:99027800-99030800	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr10:99027800-99045600	Weak transcription	Fetal Thymus	thymus
46	chr10:99028400-99038200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr10:99028600-99051200	Weak transcription	Small Intestine	intestine
48	chr10:99028800-99030800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr10:99028800-99046800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr10:99029200-99033200	Weak transcription	Fetal Intestine Small	intestine

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