Variant report

Variant	rs574060377
Chromosome Location	chr4:1238063-1238064
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:1234455-1238081	HepG2	liver:	n/a	n/a
2	MYC	chr4:1237912-1238120	MCF-7	breast:	n/a	n/a
3	POLR2A	chr4:1237730-1238659	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:1237830-1238084	GM12878	blood:	n/a	n/a
5	ESR1	chr4:1237888-1238156	T-47D	breast:	n/a	n/a
6	POLR2A	chr4:1237758-1238513	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:1236665..1239012-chr4:1297497..1299590,2	K562	blood:
2	chr4:1215883..1221793-chr4:1233494..1238232,6	K562	blood:
3	chr4:1207048..1210414-chr4:1237792..1241348,3	K562	blood:
4	chr4:1236833..1250005-chr4:1276188..1292579,54	MCF-7	breast:
5	chr4:1236808..1249320-chr4:1336333..1343819,66	MCF-7	breast:
6	chr4:1238043..1241970-chr4:1281719..1285287,6	MCF-7	breast:
7	chr4:1049115..1051492-chr4:1235735..1239693,3	MCF-7	breast:
8	chr4:1235141..1249133-chr4:1336906..1347308,118	MCF-7	breast:
9	chr4:1236923..1239811-chr4:1291885..1294129,2	K562	blood:
10	chr4:1104788..1106753-chr4:1236973..1238872,2	K562	blood:
11	chr4:990681..994690-chr4:1238010..1243594,6	MCF-7	breast:
12	chr4:1184548..1187736-chr4:1238018..1240467,3	MCF-7	breast:
13	chr4:1238004..1248980-chr4:1275065..1286840,30	K562	blood:
14	chr4:1238004..1246805-chr4:1279798..1288475,25	K562	blood:
15	chr4:1205790..1207359-chr4:1237048..1239471,2	K562	blood:

No data

Variant related genes	Relation type
CTBP1	TF binding region
ENSG00000163945	Chromatin interaction
ENSG00000159692	Chromatin interaction
ENSG00000090316	Chromatin interaction
ENSG00000127415	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:33 , 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	nsv878329	chr4:1147407-1254930	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	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
8	nsv878331	chr4:1159680-1254930	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv461153	chr4:1174861-1254930	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
12	nsv593279	chr4:1174861-1254930	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
13	nsv461154	chr4:1179213-1254930	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
14	nsv593280	chr4:1179213-1254930	Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
15	nsv878332	chr4:1179213-1254930	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
16	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
17	nsv878333	chr4:1193832-1254930	Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	esv1844406	chr4:1230397-1243775	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
28	esv1836927	chr4:1231363-1244037	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
29	esv1838677	chr4:1231540-1274734	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
30	nsv822433	chr4:1232688-1246206	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
31	nsv878334	chr4:1232910-1254930	Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
32	esv1839490	chr4:1237014-1254930	Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
33	nsv878335	chr4:1237014-1254930	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1214400-1238400	Strong transcription	Thymus	Thymus
2	chr4:1219000-1240200	Weak transcription	Hela-S3	cervix
3	chr4:1221600-1240200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:1222000-1240800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:1225000-1240200	Weak transcription	K562	blood
6	chr4:1228400-1240000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:1228800-1239400	Weak transcription	Fetal Brain Male	brain
8	chr4:1229200-1240400	Weak transcription	Fetal Kidney	kidney
9	chr4:1229600-1239600	Weak transcription	HSMM	muscle
10	chr4:1230000-1238200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:1230000-1240400	Weak transcription	HSMMtube	muscle
12	chr4:1233400-1240600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:1234000-1238800	Weak transcription	NH-A	brain
14	chr4:1234200-1239400	Weak transcription	Osteobl	bone
15	chr4:1234600-1240400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:1234600-1240800	Genic enhancers	Spleen	Spleen
17	chr4:1234800-1238800	Weak transcription	HMEC	breast
18	chr4:1234800-1240000	Genic enhancers	Fetal Intestine Large	intestine
19	chr4:1235000-1239800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:1235000-1240800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:1235000-1241200	Weak transcription	Aorta	Aorta
22	chr4:1235200-1238200	Weak transcription	HepG2	liver
23	chr4:1235200-1238600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:1235200-1238600	Enhancers	Duodenum Mucosa	Duodenum
25	chr4:1235200-1240000	Weak transcription	A549	lung
26	chr4:1235200-1240000	Weak transcription	HUVEC	blood vessel
27	chr4:1235200-1240200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr4:1235200-1240400	Enhancers	Liver	Liver
29	chr4:1235200-1240800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:1235400-1239000	Weak transcription	NHEK	skin
31	chr4:1235400-1240200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:1235400-1240200	Enhancers	Left Ventricle	heart
33	chr4:1235400-1240600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:1235400-1240600	Genic enhancers	Fetal Muscle Leg	muscle
35	chr4:1235400-1240800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:1235400-1241000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr4:1235600-1238200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:1235600-1238600	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr4:1235600-1240200	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr4:1235600-1240200	Enhancers	Right Ventricle	heart
41	chr4:1235600-1240400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr4:1235600-1240400	Genic enhancers	Fetal Muscle Trunk	muscle
43	chr4:1235600-1240600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr4:1235600-1240600	Enhancers	Right Atrium	heart
45	chr4:1235600-1241000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr4:1235600-1241000	Enhancers	Ovary	ovary
47	chr4:1235800-1239800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr4:1235800-1240200	Enhancers	Adipose Nuclei	Adipose
49	chr4:1235800-1240200	Enhancers	Brain Substantia Nigra	brain
50	chr4:1235800-1240200	Enhancers	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links