Variant report

Variant	rs4442796
Chromosome Location	chr16:69788108-69788109
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	SMC3	chr16:69788101-69788210	HepG2	liver:	n/a	n/a
2	NR2F2	chr16:69787951-69789284	K562	blood:	n/a	n/a
3	SIX5	chr16:69788023-69789195	A549	lung:	n/a	n/a
4	PML	chr16:69788007-69789165	GM12878	blood:	n/a	n/a
5	MXI1	chr16:69788085-69789120	Hela-S3	cervix:	n/a	n/a
6	MXI1	chr16:69788098-69789148	GM12878	blood:	n/a	n/a
7	MYC	chr16:69788030-69789069	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT5A	chr16:69788080-69789143	GM12878	blood:	n/a	n/a
9	NRF1	chr16:69787938-69789365	SK-N-SH	brain:	n/a	chr16:69788960-69788971 chr16:69789000-69789009 chr16:69788835-69788849 chr16:69788960-69788971 chr16:69788832-69788846 chr16:69788960-69788969 chr16:69788976-69788985 chr16:69788927-69788938 chr16:69788835-69788844 chr16:69788837-69788846 chr16:69788957-69788971 chr16:69788835-69788846 chr16:69788960-69788974 chr16:69788962-69788971
10	SMC3	chr16:69787855-69789371	SK-N-SH	brain:	n/a	chr16:69788918-69788932 chr16:69788918-69788928
11	CBX3	chr16:69788099-69789125	K562	blood:	n/a	n/a
12	MTA3	chr16:69788081-69789077	GM12878	blood:	n/a	n/a
13	MAX	chr16:69788022-69789246	HepG2	liver:	n/a	n/a
14	SIN3AK20	chr16:69788043-69789290	MCF-7	breast:	n/a	n/a
15	MXI1	chr16:69787892-69789408	IMR90	lung:	n/a	n/a
16	BCL3	chr16:69788081-69789239	A549	lung:	n/a	chr16:69788402-69788409
17	RAD21	chr16:69787939-69789356	SK-N-SH	brain:	n/a	chr16:69788447-69788457 chr16:69788438-69788450
18	MAX	chr16:69788076-69789289	A549	lung:	n/a	n/a
19	TCF12	chr16:69787850-69789287	A549	lung:	n/a	chr16:69789024-69789031
20	MYC	chr16:69788047-69789132	K562	blood:	n/a	n/a
21	TAF1	chr16:69788081-69789105	A549	lung:	n/a	n/a
22	MYC	chr16:69787958-69789258	A549	lung:	n/a	n/a
23	MYC	chr16:69788099-69789053	K562	blood:	n/a	n/a
24	MXI1	chr16:69787986-69789465	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr16:69788077-69788947	GM12878	blood:	n/a	n/a
26	RCOR1	chr16:69788093-69789182	K562	blood:	n/a	n/a
27	HCFC1	chr16:69788002-69789456	Hela-S3	cervix:	n/a	n/a
28	RCOR1	chr16:69788087-69789158	Hela-S3	cervix:	n/a	n/a
29	JUN	chr16:69788018-69789472	K562	blood:	n/a	n/a
30	RAD21	chr16:69787995-69789387	HCT-116	colon:	n/a	chr16:69788447-69788457 chr16:69788438-69788450
31	TEAD4	chr16:69787984-69789354	HepG2	liver:	n/a	n/a
32	MYBL2	chr16:69788089-69789279	HepG2	liver:	n/a	n/a
33	CTCF	chr16:69787859-69789451	A549	lung:	n/a	chr16:69788916-69788934 chr16:69788918-69788931 chr16:69788917-69788933 chr16:69788918-69788931
34	POLR2A	chr16:69788092-69789114	GM12892	blood:	n/a	n/a
35	MBD4	chr16:69787975-69789199	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:26794860..26796605-chr16:69787254..69788810,2	MCF-7	breast:
2	chr16:69598363..69600435-chr16:69788003..69790759,3	MCF-7	breast:
3	chr16:69785030..69792317-chr16:69794435..69797821,11	MCF-7	breast:
4	chr16:69787301..69791461-chr16:69794716..69798365,9	K562	blood:
5	chr16:69742300..69746801-chr16:69786779..69790470,7	MCF-7	breast:
6	chr16:69787238..69789722-chr16:69814157..69817043,3	MCF-7	breast:
7	chr16:69757296..69762552-chr16:69785671..69789636,11	K562	blood:
8	chr16:69756628..69762611-chr16:69781362..69792848,24	MCF-7	breast:
9	chr16:69741307..69747044-chr16:69787229..69790189,11	MCF-7	breast:
10	chr16:69747305..69749141-chr16:69786913..69788664,2	MCF-7	breast:
11	chr16:69758127..69765240-chr16:69786072..69790209,13	K562	blood:
12	chr16:69371724..69373455-chr16:69787462..69789118,2	K562	blood:
13	chr16:69787313..69790862-chr16:69792512..69798249,7	K562	blood:

Variant related genes	Relation type
NOB1	TF binding region
ENSG00000132603	Chromatin interaction
ENSG00000213380	Chromatin interaction
ENSG00000102908	Chromatin interaction
ENSG00000198373	Chromatin interaction
ENSG00000261602	Chromatin interaction
ENSG00000252670	Chromatin interaction
ENSG00000127870	Chromatin interaction
ENSG00000262136	Chromatin interaction
ENSG00000181019	Chromatin interaction
ENSG00000223109	Chromatin interaction
ENSG00000238683	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10400956	0.91[ASN][1000 genomes]
rs10517	0.84[CHD][hapmap];0.83[GIH][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap]
rs11075736	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1139177	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11862697	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12019048	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs12149920	0.87[ASN][1000 genomes]
rs1318651	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16958997	0.82[CHD][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs16959059	0.88[CEU][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs16959266	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2088747	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2291960	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2304526	0.82[CHD][hapmap];0.83[GIH][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs2917667	0.88[CEU][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs2917669	0.88[CEU][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.81[TSI][hapmap]
rs2917673	0.80[EUR][1000 genomes]
rs2917681	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2917682	0.84[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2917683	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2937120	0.86[ASN][1000 genomes]
rs2937123	0.86[ASN][1000 genomes]
rs2937126	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs2937127	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2965753	0.88[CEU][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs2965756	0.86[ASN][1000 genomes]
rs2965759	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2965760	0.84[ASN][1000 genomes]
rs2965761	0.84[ASN][1000 genomes]
rs2965762	0.87[ASN][1000 genomes]
rs2965763	0.87[ASN][1000 genomes]
rs2965764	0.87[ASN][1000 genomes]
rs3785075	1.00[YRI][hapmap]
rs3790084	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3790087	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3790088	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3826154	0.82[CHD][hapmap];0.86[GIH][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs4247107	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4247109	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4608327	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4619391	0.89[ASN][1000 genomes]
rs4985527	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs4985529	0.89[ASN][1000 genomes]
rs4985531	0.90[ASN][1000 genomes]
rs61090597	0.84[ASN][1000 genomes]
rs6499248	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6499249	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6499250	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6499259	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs689452	0.88[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs689456	0.80[EUR][1000 genomes]
rs7188187	0.87[ASN][1000 genomes]
rs7204615	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7359387	0.82[CHD][hapmap];0.88[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs8050369	0.89[ASN][1000 genomes]
rs8052459	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8057938	0.88[CEU][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8058594	0.86[ASN][1000 genomes]
rs8062076	0.91[ASN][1000 genomes]
rs9888980	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs9888981	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9888993	0.81[CHD][hapmap];0.83[GIH][hapmap];0.88[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs9889219	0.81[CHD][hapmap]
rs9922223	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9924953	0.81[CHD][hapmap];0.86[GIH][hapmap];0.83[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs9927105	0.91[ASN][1000 genomes]
rs9932486	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9934681	0.81[CHD][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs9936464	0.82[CHD][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs9937018	1.00[YRI][hapmap]
rs9940008	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv524364	chr16:69745145-69803443	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4442796	TMCO7	cis	cerebellum	SCAN
rs4442796	FUK	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69783600-69788200	Weak transcription	Aorta	Aorta
2	chr16:69785200-69788200	Weak transcription	Gastric	stomach
3	chr16:69785800-69788200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr16:69786800-69789200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr16:69787200-69788200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr16:69787200-69788400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr16:69787200-69788400	Flanking Active TSS	Brain Anterior Caudate	brain
8	chr16:69787200-69788600	Flanking Active TSS	Duodenum Mucosa	Duodenum
9	chr16:69787200-69788800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr16:69787200-69788800	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr16:69787200-69789000	Active TSS	H1 Cell Line	embryonic stem cell
12	chr16:69787200-69789000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr16:69787200-69789000	Active TSS	Ovary	ovary
14	chr16:69787200-69789200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr16:69787200-69789200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr16:69787200-69789200	Active TSS	Psoas Muscle	Psoas
17	chr16:69787400-69788200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr16:69787400-69788200	Active TSS	Colonic Mucosa	Colon
19	chr16:69787400-69788200	Flanking Active TSS	Dnd41	blood
20	chr16:69787400-69788400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr16:69787400-69788400	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr16:69787400-69788400	Active TSS	Right Atrium	heart
23	chr16:69787400-69788600	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr16:69787400-69788600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr16:69787400-69788800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr16:69787400-69789000	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr16:69787400-69789000	Active TSS	GM12878-XiMat	blood
28	chr16:69787400-69789200	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr16:69787400-69789200	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr16:69787400-69789200	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr16:69787400-69789200	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr16:69787400-69789200	Active TSS	Fetal Intestine Large	intestine
33	chr16:69787400-69789200	Active TSS	Right Ventricle	heart
34	chr16:69787400-69789200	Bivalent/Poised TSS	HepG2	liver
35	chr16:69787400-69789200	Active TSS	NHDF-Ad	bronchial
36	chr16:69787400-69789400	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr16:69787600-69788200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr16:69787600-69788400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr16:69787600-69788400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr16:69787600-69788400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr16:69787600-69788600	Flanking Active TSS	Fetal Thymus	thymus
42	chr16:69787600-69788800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr16:69787600-69789000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr16:69787600-69789000	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr16:69787600-69789000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr16:69787600-69789000	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr16:69787600-69789000	Active TSS	Stomach Smooth Muscle	stomach
48	chr16:69787600-69789000	Active TSS	A549	lung
49	chr16:69787600-69789000	Active TSS	HMEC	breast
50	chr16:69787600-69789000	Active TSS	NH-A	brain

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