Variant report

Variant	rs4889540
Chromosome Location	chr16:31225405-31225406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:30967372..30970193-chr16:31225350..31227883,2	MCF-7	breast:
2	chr16:31190054..31194646-chr16:31224217..31229118,11	MCF-7	breast:
3	chr16:31225327..31230953-chr16:31277531..31282411,8	MCF-7	breast:
4	chr16:31189605..31193047-chr16:31225207..31229243,8	MCF-7	breast:
5	chr16:31225061..31229339-chr16:31234222..31239323,4	MCF-7	breast:
6	chr16:31210451..31214037-chr16:31224426..31227776,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099381	Chromatin interaction
ENSG00000089280	Chromatin interaction
ENSG00000261359	Chromatin interaction
ENSG00000103490	Chromatin interaction
ENSG00000260304	Chromatin interaction
ENSG00000261925	Chromatin interaction
ENSG00000252876	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1549295	0.85[YRI][hapmap]
rs1549296	0.85[YRI][hapmap]
rs1978486	0.85[YRI][hapmap]
rs4889621	1.00[YRI][hapmap]
rs4889632	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9674226	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
4	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
5	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
6	nsv905740	chr16:31066249-31232437	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
7	nsv905741	chr16:31066249-31247924	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
8	nsv905742	chr16:31102321-31247924	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	188 gene(s)	inside rSNPs	diseases
9	nsv905744	chr16:31216517-31234288	Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv905745	chr16:31216517-31247924	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv571822	chr16:31216909-31225405	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv571823	chr16:31216909-31227908	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
13	nsv1066073	chr16:31219071-31278572	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
14	nsv571824	chr16:31220577-31225405	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	nsv905746	chr16:31223549-31237920	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4889540	TRIM72	cis	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31219000-31226400	Weak transcription	K562	blood
2	chr16:31223800-31225800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr16:31224800-31225600	Bivalent Enhancer	Fetal Intestine Large	intestine
4	chr16:31225000-31225600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr16:31225000-31225600	Flanking Active TSS	HSMMtube	muscle
6	chr16:31225000-31225800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr16:31225000-31226000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
8	chr16:31225000-31226400	Enhancers	Primary B cells from peripheral blood	blood
9	chr16:31225000-31227200	Active TSS	H9 Cell Line	embryonic stem cell
10	chr16:31225200-31225600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
11	chr16:31225200-31225800	Enhancers	Fetal Intestine Small	intestine
12	chr16:31225200-31226000	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr16:31225200-31226400	Enhancers	Primary B cells from cord blood	blood
14	chr16:31225200-31226400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
15	chr16:31225200-31226600	Enhancers	GM12878-XiMat	blood
16	chr16:31225200-31227000	Active TSS	HSMM	muscle
17	chr16:31225400-31225600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
18	chr16:31225400-31225600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
19	chr16:31225400-31225600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
20	chr16:31225400-31225600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
21	chr16:31225400-31225600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr16:31225400-31225600	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr16:31225400-31225600	Bivalent Enhancer	HepG2	liver
24	chr16:31225400-31225800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
25	chr16:31225400-31225800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr16:31225400-31225800	Weak transcription	Spleen	Spleen
27	chr16:31225400-31226000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
28	chr16:31225400-31226000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
29	chr16:31225400-31226200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr16:31225400-31226200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr16:31225400-31226200	Enhancers	Gastric	stomach
32	chr16:31225400-31226200	Enhancers	Right Ventricle	heart
33	chr16:31225400-31226400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr16:31225400-31226400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
35	chr16:31225400-31226400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr16:31225400-31226600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr16:31225400-31226800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
38	chr16:31225400-31226800	Enhancers	Fetal Heart	heart
39	chr16:31225400-31227200	Active TSS	Psoas Muscle	Psoas
40	chr16:31225400-31227800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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