Variant report

Variant	rs4489970
Chromosome Location	chr15:76631027-76631028
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	USF2	chr15:76630927-76631096	HepG2	liver:	n/a	n/a
2	CBX3	chr15:76630465-76631197	K562	blood:	n/a	n/a
3	MYC	chr15:76628173-76631136	K562	blood:	n/a	chr15:76628207-76628217 chr15:76630256-76630266 chr15:76628939-76628949
4	POLR2A	chr15:76628957-76633759	H1-neurons	neurons:	n/a	n/a
5	MYC	chr15:76629582-76631183	NB4	blood:	n/a	chr15:76630256-76630266
6	TEAD4	chr15:76630518-76631241	K562	blood:	n/a	n/a
7	CCNT2	chr15:76628112-76631050	K562	blood:	n/a	chr15:76628209-76628218 chr15:76629304-76629313 chr15:76630348-76630357 chr15:76629900-76629909
8	MAX	chr15:76629517-76631186	K562	blood:	n/a	chr15:76630256-76630266
9	MXI1	chr15:76627471-76631959	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr15:76629582-76631068	K562	blood:	n/a	n/a
11	EP300	chr15:76630968-76631180	HepG2	liver:	n/a	n/a
12	UBTF	chr15:76629552-76631028	K562	blood:	n/a	n/a
13	KAP1	chr15:76629100-76631201	HEK293	kidney:	n/a	n/a
14	POLR2A	chr15:76629100-76631702	K562	blood:	n/a	n/a
15	POLR2A	chr15:76628161-76631176	NB4	blood:	n/a	n/a
16	POLR2A	chr15:76629601-76631188	HepG2	liver:	n/a	n/a
17	JUN	chr15:76627963-76631858	K562	blood:	n/a	chr15:76628895-76628904
18	POLR2A	chr15:76629594-76631229	HL-60	blood:	n/a	n/a
19	POLR2A	chr15:76630590-76631160	HepG2	liver:	n/a	n/a
20	HCFC1	chr15:76630735-76631086	K562	blood:	n/a	n/a
21	SUZ12	chr15:76628987-76637136	NT2-D1	testis:	n/a	n/a
22	MAX	chr15:76629521-76631230	HepG2	liver:	n/a	chr15:76630256-76630266
23	MAX	chr15:76629630-76631240	HepG2	liver:	n/a	chr15:76630256-76630266
24	POLR2A	chr15:76627947-76631367	K562	blood:	n/a	n/a
25	E2F6	chr15:76629704-76631049	K562	blood:	n/a	chr15:76630314-76630326
26	MYC	chr15:76629664-76631202	K562	blood:	n/a	chr15:76630256-76630266
27	MAX	chr15:76630961-76631138	HepG2	liver:	n/a	n/a
28	ZNF263	chr15:76627921-76631912	HEK293-T-REx	kidney:	n/a	n/a
29	UBTF	chr15:76628134-76631136	K562	blood:	n/a	n/a
30	SUZ12	chr15:76629195-76634787	H1-hESC	embryonic stem cell:	n/a	n/a
31	TBP	chr15:76628417-76631155	K562	blood:	n/a	n/a
32	MAX	chr15:76628095-76631200	NB4	blood:	n/a	chr15:76628207-76628217 chr15:76630256-76630266 chr15:76628939-76628949
33	POLR2A	chr15:76627399-76631373	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:76601310..76610583-chr15:76618699..76634643,40	K562	blood:
2	chr15:76628671..76632944-chr15:76633969..76642252,10	MCF-7	breast:
3	chr15:76602419..76607116-chr15:76626572..76631104,6	MCF-7	breast:
4	chr15:76574110..76576498-chr15:76629872..76632197,2	K562	blood:
5	chr15:76601574..76614388-chr15:76623703..76634730,38	K562	blood:
6	chr15:76627980..76632315-chr15:76633215..76636196,5	MCF-7	breast:
7	chr15:76482689..76486583-chr15:76628039..76631365,3	K562	blood:
8	chr15:76630323..76632934-chr15:77355490..77357171,2	K562	blood:
9	chr15:76630618..76633246-chr15:76671829..76673785,2	K562	blood:

Variant related genes	Relation type
ENSG00000270036	TF binding region
ENSG00000169758	Chromatin interaction
ENSG00000270036	Chromatin interaction
ENSG00000140374	Chromatin interaction
ENSG00000259514	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11858964	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810348	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2456033	0.81[EUR][1000 genomes]
rs2456040	0.82[EUR][1000 genomes]
rs2456042	0.82[EUR][1000 genomes]
rs2456063	0.86[EUR][1000 genomes]
rs2456066	0.86[EUR][1000 genomes]
rs2456067	0.87[EUR][1000 genomes]
rs2456070	0.83[EUR][1000 genomes]
rs2456074	0.86[EUR][1000 genomes]
rs2460158	0.86[EUR][1000 genomes]
rs2469211	0.86[EUR][1000 genomes]
rs2469212	0.86[EUR][1000 genomes]
rs2469214	0.87[EUR][1000 genomes]
rs2469215	0.88[EUR][1000 genomes]
rs2469216	0.88[EUR][1000 genomes]
rs2469533	0.81[EUR][1000 genomes]
rs2469538	0.86[EUR][1000 genomes]
rs2469539	0.86[EUR][1000 genomes]
rs2469552	0.88[EUR][1000 genomes]
rs2469573	0.86[EUR][1000 genomes]
rs2956875	0.86[EUR][1000 genomes]
rs2959846	0.80[EUR][1000 genomes]
rs4636879	0.82[ASN][1000 genomes]
rs4886490	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495200	0.88[EUR][1000 genomes]
rs7180257	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042255	0.86[EUR][1000 genomes]
rs874223	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874224	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904399	chr15:76622903-76646575	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv827391	chr15:76626571-76636327	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv3398970	chr15:76629522-76632070	Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4489970	ISL2	cis	Whole Blood	GTEx
rs4489970	ISL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76627400-76635400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr15:76627600-76631200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:76627600-76632400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
4	chr15:76627600-76634400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
5	chr15:76628000-76631800	Bivalent/Poised TSS	Fetal Stomach	stomach
6	chr15:76628000-76632000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
7	chr15:76628200-76631200	Active TSS	HSMM	muscle
8	chr15:76628800-76631200	Bivalent Enhancer	Fetal Heart	heart
9	chr15:76628800-76631200	Bivalent Enhancer	Fetal Lung	lung
10	chr15:76628800-76631200	Bivalent Enhancer	Lung	lung
11	chr15:76629000-76633600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
12	chr15:76629200-76631200	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr15:76629200-76631400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:76629200-76632200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:76629200-76632200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr15:76629200-76632600	Bivalent Enhancer	Fetal Thymus	thymus
17	chr15:76629400-76631200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:76629400-76631200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
19	chr15:76629400-76632000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
20	chr15:76629400-76633400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
21	chr15:76629600-76631200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
22	chr15:76629600-76631400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
23	chr15:76629600-76631400	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
24	chr15:76629600-76632000	Bivalent Enhancer	Spleen	Spleen
25	chr15:76629600-76632200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr15:76629800-76631200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:76629800-76631800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:76629800-76632800	Bivalent Enhancer	Stomach Mucosa	stomach
29	chr15:76630000-76631200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
30	chr15:76630000-76632200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
31	chr15:76630200-76631400	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:76630200-76632200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:76630200-76632200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
34	chr15:76630200-76641800	Weak transcription	A549	lung
35	chr15:76630400-76631200	Flanking Active TSS	Gastric	stomach
36	chr15:76630400-76632600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
37	chr15:76630400-76636400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:76630600-76631200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:76630600-76631200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
40	chr15:76630600-76631200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:76630600-76631200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
42	chr15:76630600-76632200	Bivalent Enhancer	Brain Hippocampus Middle	brain
43	chr15:76630600-76632400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:76630600-76635600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:76630800-76631200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
46	chr15:76630800-76631200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
47	chr15:76630800-76631200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:76630800-76631200	Bivalent Enhancer	Brain Substantia Nigra	brain
49	chr15:76630800-76631200	Bivalent Enhancer	Fetal Brain Female	brain
50	chr15:76630800-76631400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood

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