Variant report

Variant	rs2099754
Chromosome Location	chr16:30756349-30756350
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr16:30756273-30756742	HepG2	liver:	n/a	n/a
2	FOXA1	chr16:30756261-30756719	HepG2	liver:	n/a	n/a
3	FOXA1	chr16:30756260-30756843	HepG2	liver:	n/a	n/a
4	MYBL2	chr16:30756257-30756881	HepG2	liver:	n/a	n/a
5	MYBL2	chr16:30756311-30756898	HepG2	liver:	n/a	n/a
6	FOXA1	chr16:30756339-30756887	HepG2	liver:	n/a	n/a
7	EP300	chr16:30756315-30756883	HepG2	liver:	n/a	n/a
8	HNF4G	chr16:30756318-30756810	HepG2	liver:	n/a	chr16:30756588-30756603

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:30756300-30756350	ProgFib	skin:	n/a
2	chr16:30756300-30756350	SK-N-SH_RA	brain:	n/a
3	chr16:30756300-30756350	HRCEpiC	kidney:	n/a
4	chr16:30756300-30756350	MCF10A-Er-Src	breast:	n/a
5	chr16:30756300-30756350	Caco-2	colon:	n/a
6	chr16:30756300-30756350	HRPEpiC	eye:	n/a
7	chr16:30756300-30756350	PFSK-1	brain:	n/a
8	chr16:30756300-30756350	GM12891	blood:	n/a
9	chr16:30756300-30756350	MCF-7	breast:	n/a
10	chr16:30756300-30756350	AoSMC	blood vessel:	n/a
11	chr16:30756300-30756350	ECC-1	luminal epithelium:	n/a
12	chr16:30756300-30756350	SAEC	small airway:	n/a
13	chr16:30756300-30756350	NHBE	bronchial:	n/a
14	chr16:30756300-30756350	HCT-116	colon:	n/a
15	chr16:30756300-30756350	HEEpiC	esophagus:	n/a
16	chr16:30756300-30756350	U87	brain:	n/a
17	chr16:30756300-30756350	GM12892	blood:	n/a
18	chr16:30756300-30756350	Hela-S3	cervix:	n/a
19	chr16:30756300-30756350	AG10803	skin:	n/a
20	chr16:30756300-30756350	HIPEpiC	eye:	n/a
21	chr16:30756300-30756350	SK-N-MC	brain:	n/a
22	chr16:30756300-30756350	CMK	blood:	n/a
23	chr16:30756300-30756350	HCPEpiC	choroid plexus:	n/a
24	chr16:30756300-30756350	BE2_C	brain:	n/a
25	chr16:30756300-30756350	PANC-1	pancreas:	n/a
26	chr16:30756300-30756350	GM12878	blood:	n/a
27	chr16:30756300-30756350	HCF	heart:	n/a
28	chr16:30756300-30756350	Hepatocyte	liver:	n/a
29	chr16:30756300-30756350	IMR90	lung:	fetal
30	chr16:30756300-30756350	HUVEC	blood vessel:	n/a
31	chr16:30756300-30756350	HepG2	liver:	n/a
32	chr16:30756300-30756350	AG09309	skin:	n/a
33	chr16:30756300-30756350	HAEpiC	amniotic membrane:	n/a
34	chr16:30756300-30756350	HL-60	blood:	n/a
35	chr16:30756300-30756350	RPTEC	kidney:	n/a
36	chr16:30756300-30756350	Jurkat	blood:	n/a
37	chr16:30756300-30756350	NH-A	brain:	n/a
38	chr16:30756300-30756350	HRE	kidney:	n/a
39	chr16:30756300-30756350	NT2-D1	testis:	n/a
40	chr16:30756300-30756350	HNPCEpiC	eye:	n/a
41	chr16:30756300-30756350	T-47D	breast:	n/a
42	chr16:30756300-30756350	GM06990	blood:	n/a
43	chr16:30756300-30756350	SKMC	muscle:	n/a
44	chr16:30756300-30756350	AG04449	skin:	fetal
45	chr16:30756300-30756350	AG04450	lung:	fetal
46	chr16:30756300-30756350	HCM	heart:	n/a
47	chr16:30756300-30756350	H1-hESC	embryonic stem cell:	embryo
48	chr16:30756300-30756350	HEK293	kidney:	embryo
49	chr16:30756300-30756350	LNCaP	prostate:	n/a
50	chr16:30756300-30756350	K562	blood:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30669052..30671027-chr16:30755746..30757539,2	MCF-7	breast:
2	chr16:30716255..30718960-chr16:30754662..30756906,2	MCF-7	breast:
3	chr16:30749452..30756439-chr16:30756844..30761929,14	K562	blood:
4	chr16:30749452..30756542-chr16:30785692..30792123,12	MCF-7	breast:
5	chr16:30749130..30756602-chr16:30770748..30777685,19	MCF-7	breast:
6	chr16:30738148..30741438-chr16:30755814..30759116,3	K562	blood:

No data

Variant related genes	Relation type
PHKG2	TF binding region
PHKG2	CpG island
ENSG00000196118	Chromatin interaction
ENSG00000262026	Chromatin interaction
ENSG00000156873	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000103549	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10782000	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs11150594	1.00[AMR][1000 genomes]
rs11150595	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs11648654	1.00[AMR][1000 genomes]
rs12596375	1.00[ASW][hapmap];0.95[LWK][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12596394	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12598056	1.00[AMR][1000 genomes]
rs12931844	1.00[AMR][1000 genomes]
rs12933849	1.00[AMR][1000 genomes]
rs1530203	1.00[ASW][hapmap];0.80[MKK][hapmap];0.83[YRI][hapmap]
rs1550477	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2053426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2099755	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2919427	0.89[ASW][hapmap]
rs2919429	0.87[ASW][hapmap]
rs2919430	1.00[AMR][1000 genomes]
rs2919431	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2919432	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs2919433	1.00[AMR][1000 genomes]
rs2972804	1.00[AMR][1000 genomes]
rs2972808	0.82[YRI][hapmap]
rs2972809	0.81[YRI][hapmap]
rs2972815	1.00[AMR][1000 genomes]
rs4617878	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4889488	1.00[AMR][1000 genomes]
rs4889494	1.00[AMR][1000 genomes]
rs4889500	0.87[ASW][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889501	1.00[AMR][1000 genomes]
rs4889503	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889504	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4889505	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889508	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs4889509	1.00[ASW][hapmap];0.95[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs4889510	1.00[AMR][1000 genomes]
rs4889528	1.00[AMR][1000 genomes]
rs55635617	1.00[AMR][1000 genomes]
rs56038936	1.00[AMR][1000 genomes]
rs56209507	1.00[AMR][1000 genomes]
rs57225118	1.00[AMR][1000 genomes]
rs57643871	1.00[AMR][1000 genomes]
rs57877247	1.00[AMR][1000 genomes]
rs6565198	0.83[YRI][hapmap]
rs6565203	1.00[AMR][1000 genomes]
rs6565204	1.00[AMR][1000 genomes]
rs6565205	1.00[AMR][1000 genomes]
rs6565208	0.87[ASW][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs6565209	1.00[AMR][1000 genomes]
rs6565210	1.00[AMR][1000 genomes]
rs7185136	0.87[ASW][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7188077	0.89[ASW][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7193412	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7194763	1.00[AMR][1000 genomes]
rs7195583	0.87[ASW][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7195612	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs73524581	1.00[AMR][1000 genomes]
rs73524584	1.00[AMR][1000 genomes]
rs73536457	1.00[AMR][1000 genomes]
rs73536466	1.00[AMR][1000 genomes]
rs73536474	1.00[AMR][1000 genomes]
rs73536488	1.00[AMR][1000 genomes]
rs73536498	1.00[AMR][1000 genomes]
rs73536499	1.00[AMR][1000 genomes]
rs8045484	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs8045550	1.00[AMR][1000 genomes]
rs8045624	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs8046609	1.00[AMR][1000 genomes]
rs8047743	1.00[AMR][1000 genomes]
rs8048656	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs8049589	1.00[AMR][1000 genomes]
rs8050578	0.93[YRI][hapmap];1.00[AMR][1000 genomes]
rs8056105	0.86[AFR][1000 genomes]
rs8058475	1.00[AMR][1000 genomes]
rs893926	0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs893927	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9921630	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9926855	0.81[AFR][1000 genomes]
rs9934046	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9941201	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9941300	0.87[ASW][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv469724	chr16:30632445-30840263	Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv482704	chr16:30632445-30840263	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
5	nsv833188	chr16:30632446-30840263	Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
6	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
7	nsv905728	chr16:30642867-30928970	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	171 gene(s)	inside rSNPs	diseases
8	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
9	esv1825223	chr16:30669091-30971810	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
10	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30711400-30757000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr16:30711800-30757000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr16:30711800-30757200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:30712000-30756600	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr16:30712200-30757400	Strong transcription	Fetal Stomach	stomach
6	chr16:30712200-30758800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr16:30721600-30756800	Strong transcription	Fetal Thymus	thymus
8	chr16:30727600-30757000	Strong transcription	Dnd41	blood
9	chr16:30728800-30757000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr16:30736400-30757000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr16:30736600-30757000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr16:30737400-30757000	Strong transcription	Fetal Brain Female	brain
13	chr16:30740600-30757000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr16:30740600-30757000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr16:30740800-30757000	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr16:30741000-30756800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr16:30741000-30757000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr16:30741000-30759000	Weak transcription	Fetal Brain Male	brain
19	chr16:30741600-30757000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr16:30743200-30757000	Strong transcription	GM12878-XiMat	blood
21	chr16:30748000-30758800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr16:30749400-30758600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr16:30749400-30758800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr16:30749800-30758600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr16:30749800-30759000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr16:30750400-30758800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr16:30750600-30759000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr16:30751000-30759000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr16:30751000-30759000	Weak transcription	Small Intestine	intestine
30	chr16:30751200-30758800	Weak transcription	Psoas Muscle	Psoas
31	chr16:30751200-30759000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr16:30751400-30758800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr16:30752000-30756800	Strong transcription	Fetal Muscle Leg	muscle
34	chr16:30752400-30756800	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr16:30752400-30756800	Strong transcription	K562	blood
36	chr16:30752400-30757000	Strong transcription	Primary T cells from cord blood	blood
37	chr16:30752400-30758800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr16:30752400-30759000	Weak transcription	Fetal Kidney	kidney
39	chr16:30752600-30757000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr16:30752600-30757000	Strong transcription	Fetal Intestine Large	intestine
41	chr16:30753000-30756800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr16:30753000-30756800	Strong transcription	Brain Anterior Caudate	brain
43	chr16:30753000-30757000	Strong transcription	Brain Hippocampus Middle	brain
44	chr16:30753200-30756600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr16:30753200-30757000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr16:30753200-30758800	Weak transcription	Right Atrium	heart
47	chr16:30753200-30759000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr16:30753200-30759000	Weak transcription	Aorta	Aorta
49	chr16:30753400-30756600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr16:30753400-30756800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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