Variant report

Variant	rs4967696
Chromosome Location	chr16:47008723-47008724
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	chr16:47006279-47008925	GM12878	blood:	n/a	n/a
2	POLR2A	chr16:47006406-47008908	Raji	blood:	n/a	n/a
3	POLR2A	chr16:47008226-47008840	GM12892	blood:	n/a	n/a
4	POLR2A	chr16:47008174-47008881	GM12878	blood:	n/a	n/a
5	POLR2A	chr16:47008126-47008777	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr16:47006263-47008909	GM18505	blood:	n/a	n/a
7	MAX	chr16:47007274-47008769	HCT-116	colon:	n/a	chr16:47008457-47008468 chr16:47008377-47008387
8	POLR2A	chr16:47006578-47008985	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr16:47006765-47008750	K562	blood:	n/a	n/a
10	POLR2A	chr16:47008224-47008755	GM12892	blood:	n/a	n/a
11	PML	chr16:47006247-47008765	GM12878	blood:	n/a	n/a
12	POLR2A	chr16:47006105-47008953	GM12878	blood:	n/a	n/a
13	POLR2A	chr16:47006129-47008902	HepG2	liver:	n/a	n/a
14	POLR2A	chr16:47006029-47008800	GM12892	blood:	n/a	n/a
15	POLR2A	chr16:47006167-47008946	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr16:47008148-47009012	GM12878	blood:	n/a	n/a
17	EP300	chr16:47008614-47008791	K562	blood:	n/a	n/a
18	POLR2A	chr16:47007317-47008797	HepG2	liver:	n/a	n/a
19	MTA3	chr16:47007295-47008786	GM12878	blood:	n/a	n/a
20	POLR2A	chr16:47008134-47008782	GM12892	blood:	n/a	n/a
21	POLR2A	chr16:47008306-47008875	K562	blood:	n/a	n/a
22	POLR2A	chr16:47008220-47008741	GM12891	blood:	n/a	n/a
23	POLR2A	chr16:47008206-47008772	GM12891	blood:	n/a	n/a
24	MYC	chr16:47006233-47008777	NB4	blood:	n/a	chr16:47006377-47006384 chr16:47006376-47006385 chr16:47008457-47008468 chr16:47008377-47008387
25	MAX	chr16:47006207-47008742	A549	lung:	n/a	chr16:47006377-47006384 chr16:47006376-47006385 chr16:47008457-47008468 chr16:47008377-47008387
26	MAX	chr16:47006190-47008747	NB4	blood:	n/a	chr16:47006377-47006384 chr16:47006376-47006385 chr16:47008457-47008468 chr16:47008377-47008387
27	POLR2A	chr16:47006000-47009011	GM12891	blood:	n/a	n/a
28	WRNIP1	chr16:47008296-47008742	GM12878	blood:	n/a	n/a
29	POLR2A	chr16:47008524-47008767	GM12878	blood:	n/a	n/a
30	POLR2A	chr16:47006416-47008747	GM19099	blood:	n/a	n/a
31	POLR2A	chr16:47006507-47008839	HepG2	liver:	n/a	n/a
32	MXI1	chr16:47005625-47008873	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr16:47008220-47008923	HCT-116	colon:	n/a	n/a
34	POLR2A	chr16:47007374-47008896	K562	blood:	n/a	n/a
35	POLR2A	chr16:47005953-47008947	H1-hESC	embryonic stem cell:	n/a	n/a
36	HEY1	chr16:47006277-47008728	HepG2	liver:	n/a	chr16:47007356-47007371 chr16:47007592-47007607 chr16:47007550-47007565 chr16:47007910-47007925
37	MYC	chr16:47007216-47008909	A549	lung:	n/a	chr16:47008457-47008468 chr16:47008377-47008387
38	POLR2A	chr16:47008300-47008975	SK-N-MC	brain:	n/a	n/a
39	POLR2A	chr16:47006494-47008920	GM12892	blood:	n/a	n/a
40	POLR2A	chr16:47006681-47008795	GM19193	blood:	n/a	n/a
41	POLR2A	chr16:47006487-47008758	GM18526	blood:	n/a	n/a
42	POLR2A	chr16:47006462-47008844	GM18951	blood:	n/a	n/a
43	POLR2A	chr16:47006245-47008747	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:47005665..47009288-chr16:47176479..47179650,5	K562	blood:
2	chr16:47007838..47011337-chr16:47047601..47050592,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPT2-1	chr16:47007627-47010136	NONHSAT142273

Variant related genes	Relation type
DNAJA2	TF binding region
ENSG00000259983	Chromatin interaction
ENSG00000260281	Chromatin interaction
ENSG00000171208	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10459877	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11247542	0.97[EUR][1000 genomes]
rs11247543	0.83[EUR][1000 genomes]
rs11859515	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445492	0.94[EUR][1000 genomes]
rs12447719	0.97[EUR][1000 genomes]
rs12596824	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12719759	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12925296	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1362406	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1376734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551188	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1894886	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978336	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2058673	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341648	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35405784	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4577108	0.97[EUR][1000 genomes]
rs4625742	0.89[EUR][1000 genomes]
rs4966781	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966794	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4966795	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4966800	0.97[EUR][1000 genomes]
rs4967664	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4967724	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4967726	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4967727	0.84[AMR][1000 genomes]
rs4967739	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62059134	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7189628	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7199379	0.97[EUR][1000 genomes]
rs7199772	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7202325	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203206	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046142	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047353	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8052160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054039	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8058144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8058714	0.83[EUR][1000 genomes]
rs8060193	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9745921	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923192	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925290	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9925525	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9927843	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1059147	chr16:46500740-47010960	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv542909	chr16:46500740-47010960	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	esv3439120	chr16:47006276-47008824	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:47008000-47008800	Flanking Active TSS	Primary T cells from cord blood	blood
2	chr16:47008000-47008800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
3	chr16:47008000-47008800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr16:47008000-47008800	Flanking Active TSS	A549	lung
5	chr16:47008000-47008800	Flanking Active TSS	Dnd41	blood
6	chr16:47008000-47008800	Flanking Active TSS	Hela-S3	cervix
7	chr16:47008200-47008800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr16:47008200-47008800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr16:47008200-47008800	Flanking Active TSS	Brain Angular Gyrus	brain
10	chr16:47008200-47008800	Flanking Active TSS	Fetal Lung	lung
11	chr16:47008200-47008800	Flanking Active TSS	Fetal Thymus	thymus
12	chr16:47008200-47008800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr16:47008200-47008800	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr16:47008200-47008800	Flanking Active TSS	Thymus	Thymus
15	chr16:47008200-47008800	Flanking Active TSS	K562	blood
16	chr16:47008400-47008800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr16:47008400-47008800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr16:47008400-47008800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr16:47008400-47008800	Enhancers	Adipose Nuclei	Adipose
20	chr16:47008400-47008800	Enhancers	Fetal Intestine Small	intestine
21	chr16:47008400-47008800	Enhancers	Fetal Stomach	stomach
22	chr16:47008400-47008800	Enhancers	Psoas Muscle	Psoas
23	chr16:47008400-47008800	Enhancers	Right Ventricle	heart
24	chr16:47008400-47009000	Enhancers	Primary B cells from cord blood	blood
25	chr16:47008400-47009000	Enhancers	Primary B cells from peripheral blood	blood
26	chr16:47008400-47009400	Enhancers	Gastric	stomach
27	chr16:47008400-47010400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr16:47008600-47008800	Enhancers	H9 Cell Line	embryonic stem cell
29	chr16:47008600-47008800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr16:47008600-47008800	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr16:47008600-47008800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr16:47008600-47008800	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr16:47008600-47008800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr16:47008600-47008800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr16:47008600-47008800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr16:47008600-47008800	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr16:47008600-47008800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr16:47008600-47008800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr16:47008600-47008800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr16:47008600-47008800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr16:47008600-47008800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr16:47008600-47008800	Enhancers	Liver	Liver
43	chr16:47008600-47008800	Enhancers	Brain Cingulate Gyrus	brain
44	chr16:47008600-47008800	Enhancers	Brain Hippocampus Middle	brain
45	chr16:47008600-47008800	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr16:47008600-47008800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr16:47008600-47008800	Enhancers	Brain Substantia Nigra	brain
48	chr16:47008600-47008800	Enhancers	Colon Smooth Muscle	Colon
49	chr16:47008600-47008800	Enhancers	Duodenum Mucosa	Duodenum
50	chr16:47008600-47008800	Enhancers	Duodenum Smooth Muscle	Duodenum

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