Variant report

Variant	rs1680073
Chromosome Location	chr4:1280337-1280338
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr4:1279828-1280368	H1-hESC	embryonic stem cell:	n/a	n/a
2	SETDB1	chr4:1279949-1280430	U2OS	brain:	n/a	n/a
3	YY1	chr4:1279850-1280367	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr4:1279850-1280445	A549	lung:	n/a	n/a
5	KAP1	chr4:1279990-1280394	K562	blood:	n/a	n/a
6	CTCF	chr4:1279937-1280377	K562	blood:	n/a	n/a
7	RAD21	chr4:1279969-1280363	ECC-1	luminal epithelium:	n/a	n/a
8	CTCF	chr4:1280200-1280350	HMEC	breast:	n/a	n/a
9	CTCF	chr4:1280240-1280390	AG09309	skin:	n/a	n/a
10	TRIM28	chr4:1280124-1280349	K562	blood:	n/a	n/a
11	TRIM28	chr4:1279983-1280444	K562	blood:	n/a	n/a
12	CBX3	chr4:1279904-1280463	K562	blood:	n/a	n/a
13	CBX3	chr4:1279973-1280373	K562	blood:	n/a	n/a
14	KAP1	chr4:1279879-1280437	HEK293	kidney:	n/a	n/a
15	RAD21	chr4:1279889-1280380	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:1279366..1281863-chr4:1281921..1284803,4	MCF-7	breast:
2	chr4:1238004..1246805-chr4:1279798..1288475,25	K562	blood:
3	chr4:1238004..1248980-chr4:1275065..1286840,30	K562	blood:
4	chr4:1242091..1248517-chr4:1279714..1285424,16	MCF-7	breast:
5	chr4:1277701..1281340-chr4:1281394..1284175,9	K562	blood:
6	chr4:1236833..1250005-chr4:1276188..1292579,54	MCF-7	breast:
7	chr4:1076538..1078176-chr4:1278229..1280499,2	MCF-7	breast:
8	chr4:1266374..1269150-chr4:1278693..1281595,2	K562	blood:

No data

Variant related genes	Relation type
MAEA	TF binding region
ENSG00000090316	Chromatin interaction
ENSG00000196810	Chromatin interaction
ENSG00000159692	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10000874	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10023922	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10024013	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11247983	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs11247986	0.81[EUR][1000 genomes]
rs1128427	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs11726778	0.88[EUR][1000 genomes]
rs11727167	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs11730939	0.88[EUR][1000 genomes]
rs11735340	0.88[EUR][1000 genomes]
rs12502916	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs12508446	0.85[CEU][hapmap]
rs12509700	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12641735	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12642410	0.86[CEU][hapmap]
rs13112706	0.86[CEU][hapmap]
rs13117476	0.95[CHB][hapmap]
rs13124847	0.89[EUR][1000 genomes]
rs13125338	0.89[EUR][1000 genomes]
rs13125842	0.89[EUR][1000 genomes]
rs13128045	0.86[CEU][hapmap]
rs13134106	0.86[CEU][hapmap]
rs13149575	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs13149715	0.89[EUR][1000 genomes]
rs13149952	0.85[CEU][hapmap]
rs13150571	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs1316393	0.81[CEU][hapmap]
rs1618072	0.90[EUR][1000 genomes]
rs1620928	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1680072	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1680074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1732100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732102	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732106	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1732107	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs1732108	0.88[EUR][1000 genomes]
rs1732123	0.89[EUR][1000 genomes]
rs1732124	0.90[EUR][1000 genomes]
rs2141656	0.95[CHB][hapmap]
rs2199956	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2276903	0.82[CHB][hapmap]
rs2293630	0.83[CHB][hapmap]
rs2293633	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2293634	0.87[EUR][1000 genomes]
rs28811276	0.90[EUR][1000 genomes]
rs3755920	1.00[CEU][hapmap]
rs4246685	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs4405964	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs4428235	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs4493483	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs4493484	0.88[EUR][1000 genomes]
rs4516656	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs4519749	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs4591539	0.89[EUR][1000 genomes]
rs4642180	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs4974582	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs4974584	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4974594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62293658	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66987549	0.93[EUR][1000 genomes]
rs6826029	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6851528	0.83[EUR][1000 genomes]
rs7664474	0.96[CHB][hapmap]
rs7668661	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7670046	0.87[EUR][1000 genomes]
rs7673398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7695691	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs900027	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs900028	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs900029	0.89[EUR][1000 genomes]
rs922698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9631804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9631805	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9992932	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9992934	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
6	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
8	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
9	nsv997971	chr4:1191256-1518521	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv461155	chr4:1203265-1352685	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
11	nsv593281	chr4:1203265-1352685	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
12	nsv1002097	chr4:1212573-1320086	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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	51 gene(s)	inside rSNPs	diseases
13	nsv536986	chr4:1212573-1320086	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
14	esv1811773	chr4:1228251-1287474	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
15	esv1800629	chr4:1228451-1287274	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS 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	51 gene(s)	inside rSNPs	diseases
16	esv1812851	chr4:1228451-1287274	Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
17	esv1823612	chr4:1228451-1287274	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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	51 gene(s)	inside rSNPs	diseases
18	esv1825633	chr4:1228451-1287274	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
19	nsv593298	chr4:1244267-1342521	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
20	nsv461156	chr4:1254930-1312394	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
21	nsv593299	chr4:1254930-1312394	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
22	esv1798897	chr4:1265740-1287474	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
23	esv1833294	chr4:1265740-1287474	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
24	esv1829934	chr4:1265940-1287274	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
25	nsv593300	chr4:1272664-1312394	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
26	nsv878338	chr4:1277826-1358449	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
27	nsv878339	chr4:1277826-1363886	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
28	nsv878340	chr4:1277826-1386570	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
29	nsv878341	chr4:1277826-1391400	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1680073	CTBP1	Cis_1M	lymphoblastoid	RTeQTL
rs1680073	UVSSA	cis	Whole Blood	GTEx
rs1680073	UVSSA	cis	Artery Aorta	GTEx
rs1680073	CRIPAK	cis	Thyroid	GTEx
rs1680073	UVSSA	cis	Stomach	GTEx
rs1680073	CTBP1	cis	multi-tissue	Pritchard
rs1680073	UVSSA	cis	lung	GTEx
rs1680073	CRIPAK	cis	Artery Aorta	GTEx
rs1680073	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx
rs1680073	UVSSA	cis	Thyroid	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1245400-1282400	Weak transcription	Brain Angular Gyrus	brain
2	chr4:1245800-1282600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:1245800-1282600	Weak transcription	Right Ventricle	heart
4	chr4:1246000-1282600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr4:1254800-1282400	Weak transcription	Pancreas	Pancrea
6	chr4:1259400-1283000	Weak transcription	Ovary	ovary
7	chr4:1263400-1282600	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:1263800-1282800	Weak transcription	Brain Anterior Caudate	brain
9	chr4:1267800-1282400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr4:1270600-1282400	Weak transcription	Lung	lung
11	chr4:1278800-1281000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:1279600-1280600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
13	chr4:1280000-1280400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
14	chr4:1280000-1280400	ZNF genes & repeats	Spleen	Spleen
15	chr4:1280000-1280600	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr4:1280200-1282400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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