Variant report

Variant	rs60410862
Chromosome Location	chr4:1287597-1287598
allele	A/T
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	EBF1	chr4:1287349-1287702	GM12878	blood:	n/a	chr4:1287495-1287506
2	POLR2A	chr4:1287267-1288191	K562	blood:	n/a	n/a
3	EBF1	chr4:1287354-1287723	GM12878	blood:	n/a	chr4:1287495-1287506
4	POU2F2	chr4:1287327-1287760	GM12878	blood:	n/a	chr4:1287565-1287578
5	POU2F2	chr4:1287458-1287680	GM12878	blood:	n/a	chr4:1287565-1287578
6	RUNX3	chr4:1287346-1287671	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:1287458-1287877	GM12891	blood:	n/a	n/a
8	WRNIP1	chr4:1287525-1287725	GM12878	blood:	n/a	n/a
9	POLR2A	chr4:1287344-1287937	K562	blood:	n/a	n/a
10	POLR2A	chr4:1287311-1287780	K562	blood:	n/a	n/a
11	POLR2A	chr4:1287511-1287901	GM12878	blood:	n/a	n/a
12	RFX5	chr4:1287454-1287727	GM12878	blood:	n/a	n/a
13	POU2F2	chr4:1287377-1287712	GM12891	blood:	n/a	chr4:1287565-1287578
14	POLR2A	chr4:1287545-1287656	H1-hESC	embryonic stem cell:	n/a	n/a
15	EBF1	chr4:1287446-1287699	GM12878	blood:	n/a	chr4:1287495-1287506
16	POLR2A	chr4:1287317-1287941	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:1286127..1289218-chr4:1332032..1335159,3	K562	blood:
2	chr4:1287223..1288934-chr4:1342789..1345119,2	K562	blood:
3	chr4:1284419..1287813-chr4:1334118..1338051,4	MCF-7	breast:
4	chr4:1238004..1246805-chr4:1279798..1288475,25	K562	blood:
5	chr4:1287434..1290416-chr4:1342936..1345119,2	K562	blood:
6	chr4:1225914..1229092-chr4:1286494..1288303,3	K562	blood:
7	chr4:1282437..1287650-chr4:1338224..1344043,13	MCF-7	breast:
8	chr4:1236833..1250005-chr4:1276188..1292579,54	MCF-7	breast:
9	chr4:1265257..1267082-chr4:1285469..1287790,2	K562	blood:

Variant related genes	Relation type
MAEA	TF binding region
ENSG00000163945	Chromatin interaction
ENSG00000159692	Chromatin interaction
ENSG00000196810	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10013662	1.00[EUR][1000 genomes]
rs10024567	0.82[AFR][1000 genomes]
rs11931513	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11932230	0.81[AMR][1000 genomes]
rs11932895	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13115935	1.00[EUR][1000 genomes]
rs1383658	1.00[EUR][1000 genomes]
rs1383659	1.00[EUR][1000 genomes]
rs1481168	1.00[EUR][1000 genomes]
rs1680075	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1680082	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17164618	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1732105	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2127911	1.00[EUR][1000 genomes]
rs34082974	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4336168	1.00[EUR][1000 genomes]
rs4465987	1.00[EUR][1000 genomes]
rs4974567	1.00[EUR][1000 genomes]
rs4974580	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4974581	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4974634	1.00[EUR][1000 genomes]
rs4974636	1.00[EUR][1000 genomes]
rs4974641	1.00[EUR][1000 genomes]
rs57461362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59318613	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59669372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6818213	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6834402	1.00[EUR][1000 genomes]
rs6835204	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73069991	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73069994	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73071910	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73071925	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73073722	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73073725	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73073727	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73073729	1.00[EUR][1000 genomes]
rs73796061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7660109	1.00[EUR][1000 genomes]
rs7691582	1.00[EUR][1000 genomes]
rs922697	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	nsv1002635	chr4:1282603-1402761	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer 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	37 gene(s)	inside rSNPs	diseases
23	esv3384011	chr4:1287052-1291350	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 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	chr4:1284600-1290200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:1284800-1288400	Enhancers	Primary B cells from peripheral blood	blood
3	chr4:1285000-1287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:1285000-1289400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr4:1285200-1287600	Enhancers	Primary T cells fromperipheralblood	blood
6	chr4:1285200-1287800	Enhancers	Right Ventricle	heart
7	chr4:1285200-1290200	Weak transcription	Aorta	Aorta
8	chr4:1285200-1293800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:1285200-1303400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:1285400-1287600	Weak transcription	NH-A	brain
11	chr4:1285400-1288400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr4:1285400-1289200	Enhancers	Colon Smooth Muscle	Colon
13	chr4:1285400-1289400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr4:1285400-1290200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:1285400-1290600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr4:1285400-1291200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:1285400-1291200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr4:1285400-1293400	Weak transcription	A549	lung
19	chr4:1285400-1294200	Weak transcription	HSMMtube	muscle
20	chr4:1285400-1294200	Weak transcription	HUVEC	blood vessel
21	chr4:1285400-1302400	Weak transcription	Fetal Kidney	kidney
22	chr4:1285600-1287600	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr4:1285600-1287800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:1285600-1289400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
25	chr4:1285600-1290200	Weak transcription	Fetal Lung	lung
26	chr4:1285600-1290600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:1285600-1291400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr4:1285800-1289200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr4:1285800-1296000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr4:1285800-1302200	Weak transcription	NHDF-Ad	bronchial
31	chr4:1286000-1287600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:1286000-1288200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:1286000-1288800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr4:1286000-1288800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr4:1286000-1289400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:1286000-1289400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr4:1286000-1295200	Strong transcription	Thymus	Thymus
38	chr4:1286200-1287600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr4:1286200-1287600	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr4:1286200-1287600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr4:1286200-1287600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:1286200-1287600	Weak transcription	Stomach Mucosa	stomach
43	chr4:1286200-1287800	Strong transcription	Fetal Brain Female	brain
44	chr4:1286200-1288000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:1286200-1288000	Weak transcription	Brain Angular Gyrus	brain
46	chr4:1286200-1290200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr4:1286200-1290800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr4:1286200-1291400	Weak transcription	Hela-S3	cervix
49	chr4:1286200-1293400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:1286200-1299200	Strong transcription	Fetal Intestine Small	intestine

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