Variant report

Variant	rs55979739
Chromosome Location	chr16:31049155-31049156
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	chr16:31049091-31049301	K562	blood:	n/a	n/a
2	POLR2A	chr16:31049155-31049505	HepG2	liver:	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	chr16:30996163..30997707-chr16:31048013..31050066,2	MCF-7	breast:
4	chr16:31048921..31052492-chr16:31052504..31056345,6	MCF-7	breast:

Variant related genes	Relation type
STX4	TF binding region
ENSG00000167394	Chromatin interaction
ENSG00000167395	Chromatin interaction
ENSG00000232748	Chromatin interaction
ENSG00000099377	Chromatin interaction
ENSG00000261124	Chromatin interaction
ENSG00000268863	Chromatin interaction
ENSG00000260911	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1060506	0.84[ASN][1000 genomes]
rs10871454	0.95[ASN][1000 genomes]
rs1108431	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11150604	1.00[ASN][1000 genomes]
rs11640767	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11640957	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11642003	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11642192	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11647284	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11647442	0.84[ASN][1000 genomes]
rs11862744	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11864806	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11864839	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11865038	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11865499	0.84[ASN][1000 genomes]
rs12445650	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12448321	1.00[ASN][1000 genomes]
rs12597511	0.82[ASN][1000 genomes]
rs12716981	0.84[ASN][1000 genomes]
rs12716982	0.84[ASN][1000 genomes]
rs12934418	1.00[ASN][1000 genomes]
rs14235	0.84[ASN][1000 genomes]
rs1549293	0.84[ASN][1000 genomes]
rs17839567	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17839568	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1978485	0.84[ASN][1000 genomes]
rs1978487	0.84[ASN][1000 genomes]
rs2032915	0.84[ASN][1000 genomes]
rs2288004	1.00[ASN][1000 genomes]
rs2303222	0.89[ASN][1000 genomes]
rs2303223	0.86[ASN][1000 genomes]
rs2359612	0.89[ASN][1000 genomes]
rs2855475	0.84[ASN][1000 genomes]
rs28725459	0.81[ASN][1000 genomes]
rs28814987	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2884738	0.84[ASN][1000 genomes]
rs34649473	0.83[ASN][1000 genomes]
rs34898535	0.87[ASN][1000 genomes]
rs35351013	0.82[ASN][1000 genomes]
rs35468353	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35713203	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35961830	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3751855	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4468641	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4527034	0.84[ASN][1000 genomes]
rs4889526	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4889530	0.89[ASN][1000 genomes]
rs4889609	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4889620	0.84[ASN][1000 genomes]
rs55766044	0.84[ASN][1000 genomes]
rs56284083	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56314408	0.84[ASN][1000 genomes]
rs56813533	0.82[ASN][1000 genomes]
rs57434408	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57576577	0.91[EUR][1000 genomes]
rs58726213	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59061704	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59735493	0.84[ASN][1000 genomes]
rs60996860	0.81[ASN][1000 genomes]
rs61162043	0.89[ASN][1000 genomes]
rs61320757	0.84[ASN][1000 genomes]
rs6565217	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7187995	0.82[ASN][1000 genomes]
rs7196161	0.89[ASN][1000 genomes]
rs7196726	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7197717	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7199949	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72800847	0.82[EUR][1000 genomes]
rs7294	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs729482	0.80[EUR][1000 genomes]
rs732172	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732173	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73530203	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs749670	0.89[ASN][1000 genomes]
rs749671	0.89[ASN][1000 genomes]
rs749767	0.84[ASN][1000 genomes]
rs7500176	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750952	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8047803	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8050894	0.89[ASN][1000 genomes]
rs8056842	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8061047	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs881929	0.89[ASN][1000 genomes]
rs889548	0.84[ASN][1000 genomes]
rs889555	0.84[ASN][1000 genomes]
rs9673641	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9923231	0.89[ASN][1000 genomes]
rs9925964	0.84[ASN][1000 genomes]
rs9929899	0.98[ASN][1000 genomes]
rs9934438	0.89[ASN][1000 genomes]
rs9936329	0.84[ASN][1000 genomes]
rs9939417	1.00[ASN][1000 genomes]
rs9939558	1.00[ASN][1000 genomes]
rs9972727	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs55979739	RP11-196G11.2	cis	Esophagus Muscularis	GTEx
rs55979739	STX4	Cis_1M	lymphoblastoid	RTeQTL
rs55979739	RP11-196G11.2	cis	lung	GTEx
rs55979739	STX1B	cis	Thyroid	GTEx
rs55979739	RP11-196G11.2	cis	Muscle Skeletal	GTEx
rs55979739	MYST1	Cis_1M	lymphoblastoid	RTeQTL
rs55979739	KAT8	cis	Skin Sun Exposed Lower leg	GTEx

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	chr16:31045800-31049600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr16:31045800-31053400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr16:31045800-31053400	Weak transcription	Fetal Kidney	kidney
5	chr16:31046000-31049200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr16:31046000-31049200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr16:31046000-31049200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr16:31046000-31049200	Weak transcription	Esophagus	oesophagus
9	chr16:31046000-31049200	Weak transcription	Ovary	ovary
10	chr16:31046000-31049200	Weak transcription	Psoas Muscle	Psoas
11	chr16:31046000-31049200	Weak transcription	Thymus	Thymus
12	chr16:31046000-31049400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr16:31046000-31050400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr16:31046000-31050400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr16:31046000-31053400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr16:31046000-31053400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr16:31046000-31053400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr16:31046000-31053400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr16:31046000-31053400	Strong transcription	Fetal Intestine Small	intestine
20	chr16:31046000-31071000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr16:31046000-31083200	Weak transcription	Right Atrium	heart
22	chr16:31046200-31049400	Weak transcription	Primary B cells from cord blood	blood
23	chr16:31046200-31049400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr16:31046200-31049600	Weak transcription	Fetal Brain Male	brain
25	chr16:31046200-31050400	Weak transcription	NH-A	brain
26	chr16:31046200-31051400	Strong transcription	Fetal Lung	lung
27	chr16:31046200-31051800	Strong transcription	NHLF	lung
28	chr16:31046200-31052000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr16:31046200-31052000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr16:31046200-31052400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr16:31046200-31053200	Strong transcription	Fetal Muscle Leg	muscle
32	chr16:31046200-31053400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr16:31046200-31053400	Weak transcription	Fetal Heart	heart
34	chr16:31046200-31053400	Strong transcription	Fetal Intestine Large	intestine
35	chr16:31046200-31054400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr16:31046200-31054600	Strong transcription	Dnd41	blood
37	chr16:31046200-31054800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr16:31046200-31054800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr16:31046200-31055000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr16:31046200-31055000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr16:31046200-31055000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr16:31046200-31055200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr16:31046200-31058200	Weak transcription	HUVEC	blood vessel
44	chr16:31046200-31063000	Weak transcription	Hela-S3	cervix
45	chr16:31046200-31063200	Weak transcription	HMEC	breast
46	chr16:31046400-31049200	Weak transcription	Brain Angular Gyrus	brain
47	chr16:31046400-31050400	Strong transcription	NHEK	skin
48	chr16:31046400-31051800	Strong transcription	Aorta	Aorta
49	chr16:31046400-31052000	Strong transcription	Osteobl	bone
50	chr16:31046400-31052200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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