Variant report

Variant	rs72800858
Chromosome Location	chr16:31047773-31047774
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	POLR2A	chr16:31047551-31047831	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:31047516-31048159	K562	blood:	n/a	n/a
3	POLR2A	chr16:31047629-31048214	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:31043007..31053782-chr16:31072765..31087431,40	MCF-7	breast:
2	chr16:30996080..30998597-chr16:31047419..31049250,2	K562	blood:
3	chr16:31046252..31048990-chr16:31049439..31052730,4	K562	blood:

Variant related genes	Relation type
STX4	TF binding region
ENSG00000268863	Chromatin interaction
ENSG00000167394	Chromatin interaction
ENSG00000261124	Chromatin interaction
ENSG00000099377	Chromatin interaction
ENSG00000167395	Chromatin interaction
ENSG00000232748	Chromatin interaction
ENSG00000103496	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17708472	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17881535	0.82[AMR][1000 genomes]
rs2359674	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs45599534	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55731737	0.84[EUR][1000 genomes]
rs55908605	0.84[EUR][1000 genomes]
rs6565214	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72785521	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72785525	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72785535	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72800841	0.80[EUR][1000 genomes]
rs72800842	0.83[EUR][1000 genomes]
rs72800845	0.85[EUR][1000 genomes]
rs72800846	0.84[EUR][1000 genomes]
rs72800849	0.86[EUR][1000 genomes]
rs72800854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8046978	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8047104	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9927295	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers 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	437 gene(s)	inside rSNPs	diseases
3	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
4	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
5	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
6	nsv833191	chr16:30864242-31048051	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	115 gene(s)	inside rSNPs	diseases
7	nsv905734	chr16:30877544-31191482	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
8	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
9	nsv457483	chr16:30903679-31191482	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
10	nsv571820	chr16:30903679-31191482	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
11	esv1797877	chr16:30948643-31188432	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
12	nsv833193	chr16:30960796-31133604	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
13	nsv916994	chr16:30971725-31078117	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31045600-31055800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:31045800-31048000	Genic enhancers	Spleen	Spleen
3	chr16:31045800-31049600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr16:31045800-31053400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr16:31045800-31053400	Weak transcription	Fetal Kidney	kidney
6	chr16:31046000-31048200	Strong transcription	Lung	lung
7	chr16:31046000-31048400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr16:31046000-31049000	Weak transcription	Brain Germinal Matrix	brain
9	chr16:31046000-31049000	Weak transcription	Small Intestine	intestine
10	chr16:31046000-31049200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr16:31046000-31049200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr16:31046000-31049200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr16:31046000-31049200	Weak transcription	Esophagus	oesophagus
14	chr16:31046000-31049200	Weak transcription	Ovary	ovary
15	chr16:31046000-31049200	Weak transcription	Psoas Muscle	Psoas
16	chr16:31046000-31049200	Weak transcription	Thymus	Thymus
17	chr16:31046000-31049400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr16:31046000-31050400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr16:31046000-31050400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr16:31046000-31053400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr16:31046000-31053400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr16:31046000-31053400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr16:31046000-31053400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr16:31046000-31053400	Strong transcription	Fetal Intestine Small	intestine
25	chr16:31046000-31071000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr16:31046000-31083200	Weak transcription	Right Atrium	heart
27	chr16:31046200-31047800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr16:31046200-31047800	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr16:31046200-31047800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr16:31046200-31047800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr16:31046200-31047800	Weak transcription	Colon Smooth Muscle	Colon
32	chr16:31046200-31047800	Genic enhancers	Fetal Muscle Trunk	muscle
33	chr16:31046200-31047800	Weak transcription	GM12878-XiMat	blood
34	chr16:31046200-31048000	Strong transcription	Fetal Thymus	thymus
35	chr16:31046200-31048000	Genic enhancers	Stomach Smooth Muscle	stomach
36	chr16:31046200-31048200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr16:31046200-31048200	Strong transcription	Brain Anterior Caudate	brain
38	chr16:31046200-31048200	Genic enhancers	Rectal Mucosa Donor 29	rectum
39	chr16:31046200-31048200	Strong transcription	HSMMtube	muscle
40	chr16:31046200-31048400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr16:31046200-31048400	Strong transcription	NHDF-Ad	bronchial
42	chr16:31046200-31049400	Weak transcription	Primary B cells from cord blood	blood
43	chr16:31046200-31049400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr16:31046200-31049600	Weak transcription	Fetal Brain Male	brain
45	chr16:31046200-31050400	Weak transcription	NH-A	brain
46	chr16:31046200-31051400	Strong transcription	Fetal Lung	lung
47	chr16:31046200-31051800	Strong transcription	NHLF	lung
48	chr16:31046200-31052000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr16:31046200-31052000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr16:31046200-31052400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links