Variant report

Variant	rs4886490
Chromosome Location	chr15:76628440-76628441
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	CEBPB	chr15:76628387-76629228	HepG2	liver:	n/a	n/a
2	TAF1	chr15:76628132-76628510	GM12878	blood:	n/a	n/a
3	MAX	chr15:76628380-76629274	A549	lung:	n/a	chr15:76628939-76628949
4	POLR2A	chr15:76628183-76629388	U87	brain:	n/a	n/a
5	MAX	chr15:76628190-76629450	SK-N-SH	brain:	n/a	chr15:76628207-76628217 chr15:76628939-76628949
6	MYC	chr15:76628152-76628449	H1-hESC	embryonic stem cell:	n/a	chr15:76628207-76628217
7	BCL3	chr15:76628292-76629316	A549	lung:	n/a	n/a
8	RCOR1	chr15:76628238-76629825	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr15:76627989-76629358	HCT-116	colon:	n/a	n/a
10	ATF3	chr15:76628409-76629269	K562	blood:	n/a	chr15:76628795-76628806 chr15:76628793-76628806 chr15:76628791-76628805 chr15:76628794-76628804 chr15:76629077-76629084 chr15:76629077-76629085 chr15:76629028-76629048 chr15:76629073-76629084 chr15:76629073-76629088 chr15:76628795-76628806
11	YY1	chr15:76628209-76628456	SK-N-SH_RA	brain:	n/a	chr15:76628209-76628218
12	POLR2A	chr15:76627501-76628913	H1-neurons	neurons:	n/a	n/a
13	MYC	chr15:76628173-76631136	K562	blood:	n/a	chr15:76628207-76628217 chr15:76630256-76630266 chr15:76628939-76628949
14	MAX	chr15:76628196-76629307	K562	blood:	n/a	chr15:76628207-76628217 chr15:76628939-76628949
15	SPI1	chr15:76627860-76629142	GM12878	blood:	n/a	chr15:76628752-76628761 chr15:76628753-76628760
16	HEY1	chr15:76628150-76629369	K562	blood:	n/a	chr15:76629077-76629086
17	MYBL2	chr15:76628290-76629605	HepG2	liver:	n/a	n/a
18	SP1	chr15:76628104-76629381	A549	lung:	n/a	chr15:76628961-76628971 chr15:76629040-76629049 chr15:76628960-76628971 chr15:76628960-76628972 chr15:76628209-76628218 chr15:76629039-76629051 chr15:76629040-76629054 chr15:76629041-76629050 chr15:76629039-76629051 chr15:76628940-76628954 chr15:76629304-76629314 chr15:76628210-76628219 chr15:76628205-76628219 chr15:76628961-76628970 chr15:76628208-76628220 chr15:76628961-76628970 chr15:76628962-76628971 chr15:76628210-76628219 chr15:76628960-76628972
19	POLR2A	chr15:76628230-76629149	H1-hESC	embryonic stem cell:	n/a	n/a
20	SPI1	chr15:76628047-76628454	GM12878	blood:	n/a	n/a
21	UBTF	chr15:76628434-76629312	K562	blood:	n/a	n/a
22	POLR2A	chr15:76628192-76629217	GM12892	blood:	n/a	n/a
23	PML	chr15:76628363-76629423	K562	blood:	n/a	n/a
24	SIN3AK20	chr15:76628383-76628931	A549	lung:	n/a	n/a
25	SPI1	chr15:76627934-76628636	HL-60	blood:	n/a	n/a
26	ZMIZ1	chr15:76628007-76629306	K562	blood:	n/a	n/a
27	POLR2A	chr15:76628250-76628608	GM12878	blood:	n/a	n/a
28	POLR2A	chr15:76628149-76629340	HCT-116	colon:	n/a	n/a
29	POLR2A	chr15:76627986-76629830	IMR90	lung:	n/a	n/a
30	POLR2A	chr15:76628205-76629388	U87	brain:	n/a	n/a
31	POLR2A	chr15:76628407-76629372	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr15:76628289-76629361	K562	blood:	n/a	n/a
33	POLR2A	chr15:76628198-76629319	GM19099	blood:	n/a	n/a
34	CCNT2	chr15:76628112-76631050	K562	blood:	n/a	chr15:76628209-76628218 chr15:76629304-76629313 chr15:76630348-76630357 chr15:76629900-76629909
35	POLR2A	chr15:76628271-76629358	K562	blood:	n/a	n/a
36	POLR2A	chr15:76628092-76629373	HL-60	blood:	n/a	n/a
37	POLR2A	chr15:76627540-76629356	GM12892	blood:	n/a	n/a
38	CHD2	chr15:76628142-76629327	Hela-S3	cervix:	n/a	chr15:76628990-76629000
39	YY1	chr15:76628429-76629274	A549	lung:	n/a	chr15:76628775-76628789
40	POLR2A	chr15:76628181-76629349	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr15:76628083-76629479	U87	brain:	n/a	n/a
42	MXI1	chr15:76627471-76631959	SK-N-SH	brain:	n/a	n/a
43	SIN3A	chr15:76628282-76629217	H1-hESC	embryonic stem cell:	n/a	chr15:76629043-76629056 chr15:76628714-76628723 chr15:76628384-76628395
44	GABPA	chr15:76628340-76629178	A549	lung:	n/a	n/a
45	TAF1	chr15:76628213-76629314	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr15:76628119-76629261	GM12878	blood:	n/a	n/a
47	SMARCB1	chr15:76628226-76629321	Hela-S3	cervix:	n/a	n/a
48	YY1	chr15:76628234-76628533	SK-N-SH_RA	brain:	n/a	n/a
49	ATF3	chr15:76628194-76629020	A549	lung:	n/a	chr15:76628795-76628806 chr15:76628793-76628806 chr15:76628209-76628218 chr15:76628791-76628805 chr15:76628794-76628804 chr15:76628795-76628806
50	ZKSCAN1	chr15:76628323-76629867	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:76628424-76628474	PANC-1	pancreas:	n/a
2	chr15:76628424-76628474	GM06990	blood:	n/a
3	chr15:76628424-76628474	LNCaP	prostate:	n/a
4	chr15:76628424-76628474	HIPEpiC	eye:	n/a
5	chr15:76628424-76628474	SK-N-MC	brain:	n/a
6	chr15:76628424-76628474	BJ	skin:	n/a
7	chr15:76628424-76628474	NH-A	brain:	n/a
8	chr15:76628424-76628474	MCF-7	breast:	n/a
9	chr15:76628424-76628474	HMEC	breast:	n/a
10	chr15:76628424-76628474	GM12878	blood:	n/a
11	chr15:76628424-76628474	BE2_C	brain:	n/a
12	chr15:76628424-76628474	RPTEC	kidney:	n/a
13	chr15:76628424-76628474	IMR90	lung:	fetal
14	chr15:76628424-76628474	AG09309	skin:	n/a
15	chr15:76628424-76628474	HCT-116	colon:	n/a
16	chr15:76628424-76628474	HAEpiC	amniotic membrane:	n/a
17	chr15:76628424-76628474	AoSMC	blood vessel:	n/a
18	chr15:76628424-76628474	SK-N-SH	brain:	n/a
19	chr15:76628424-76628474	K562	blood:	n/a
20	chr15:76628424-76628474	NB4	blood:	n/a
21	chr15:76628424-76628474	GM12892	blood:	n/a
22	chr15:76628424-76628474	HCF	heart:	n/a
23	chr15:76628424-76628474	SAEC	small airway:	n/a
24	chr15:76628424-76628474	AG09319	gingival:	n/a
25	chr15:76628424-76628474	MCF10A-Er-Src	breast:	n/a
26	chr15:76628424-76628474	Jurkat	blood:	n/a
27	chr15:76628424-76628474	H1-hESC	embryonic stem cell:	embryo
28	chr15:76628424-76628474	AG04450	lung:	fetal
29	chr15:76628424-76628474	GM12891	blood:	n/a
30	chr15:76628424-76628474	NHBE	bronchial:	n/a
31	chr15:76628424-76628474	HRCEpiC	kidney:	n/a
32	chr15:76628424-76628474	Hepatocyte	liver:	n/a
33	chr15:76628424-76628474	AG04449	skin:	fetal
34	chr15:76628424-76628474	A549	lung:	n/a
35	chr15:76628424-76628474	HCM	heart:	n/a
36	chr15:76628424-76628474	HUVEC	blood vessel:	n/a
37	chr15:76628424-76628474	HEK293	kidney:	embryo
38	chr15:76628424-76628474	PrEC	prostate:	n/a
39	chr15:76628424-76628474	NT2-D1	testis:	n/a
40	chr15:76628424-76628474	HepG2	liver:	n/a
41	chr15:76628424-76628474	ProgFib	skin:	n/a
42	chr15:76628424-76628474	U87	brain:	n/a
43	chr15:76628424-76628474	T-47D	breast:	n/a
44	chr15:76628424-76628474	SKMC	muscle:	n/a
45	chr15:76628424-76628474	ovcar-3	ovarian:	n/a
46	chr15:76628424-76628474	HRE	kidney:	n/a
47	chr15:76628424-76628474	AG10803	skin:	n/a
48	chr15:76628424-76628474	NHDF-neo	bronchial:	n/a
49	chr15:76628424-76628474	HCPEpiC	choroid plexus:	n/a
50	chr15:76628424-76628474	HEEpiC	esophagus:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:76601310..76610583-chr15:76618699..76634643,40	K562	blood:
2	chr15:76598820..76601362-chr15:76625646..76628540,2	K562	blood:
3	chr15:76537469..76539301-chr15:76627220..76628943,2	MCF-7	breast:
4	chr15:76600511..76607655-chr15:76613791..76629933,32	MCF-7	breast:
5	chr15:76602419..76607116-chr15:76626572..76631104,6	MCF-7	breast:
6	chr15:76597896..76600825-chr15:76626656..76628546,2	MCF-7	breast:
7	chr15:76628338..76628972-chr16:3333283..3333855,2	Hela-S3	cervix:
8	chr15:76601574..76614388-chr15:76623703..76634730,38	K562	blood:
9	chr15:76627980..76632315-chr15:76633215..76636196,5	MCF-7	breast:
10	chr15:76628182..76629017-chr6:109415644..109416177,2	Hela-S3	cervix:
11	chr15:76482689..76486583-chr15:76628039..76631365,3	K562	blood:
12	chr15:76583048..76585196-chr15:76627041..76629277,2	MCF-7	breast:
13	chr15:76628312..76628814-chr22:43010507..43011050,2	HCT-116	colon:

Variant related genes	Relation type
ISL2	TF binding region
ISL2	CpG island
ENSG00000259514	Chromatin interaction
ENSG00000140374	Chromatin interaction
ENSG00000080546	Chromatin interaction
ENSG00000100227	Chromatin interaction
ENSG00000270036	Chromatin interaction
ENSG00000169758	Chromatin interaction
ENSG00000006194	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11858964	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157760	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs157761	0.86[CEU][hapmap];0.89[CHB][hapmap]
rs157777	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs157778	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs157789	0.86[CEU][hapmap];0.89[CHB][hapmap]
rs1801591	0.86[CEU][hapmap]
rs1810348	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182253	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs2078437	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs2291449	0.86[CEU][hapmap]
rs2456033	0.81[EUR][1000 genomes]
rs2456040	0.82[EUR][1000 genomes]
rs2456042	0.82[EUR][1000 genomes]
rs2456047	0.90[GIH][hapmap]
rs2456063	0.86[EUR][1000 genomes]
rs2456066	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2456067	0.87[EUR][1000 genomes]
rs2456070	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2456074	0.86[EUR][1000 genomes]
rs2460153	1.00[CEU][hapmap]
rs2460158	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2460161	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs2469211	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2469212	0.86[EUR][1000 genomes]
rs2469214	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs2469215	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2469216	0.88[EUR][1000 genomes]
rs2469533	0.81[EUR][1000 genomes]
rs2469538	0.86[EUR][1000 genomes]
rs2469539	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2469552	0.88[EUR][1000 genomes]
rs2469554	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs2469564	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs2469573	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs283796	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs283802	0.86[CEU][hapmap];0.89[CHB][hapmap]
rs284898	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs284902	0.86[CEU][hapmap];0.89[CHB][hapmap]
rs284903	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs284904	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs284905	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs284907	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs2956875	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2957560	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs2957607	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs2957613	0.86[CEU][hapmap]
rs2959846	0.80[EUR][1000 genomes]
rs387321	0.86[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs4489970	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4636879	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs480672	0.90[CHB][hapmap]
rs4886491	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[MEX][hapmap]
rs4886492	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs494268	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs506000	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs6495200	0.88[EUR][1000 genomes]
rs7180257	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031378	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs8031672	0.82[CEU][hapmap]
rs8042255	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs874223	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4886490	ISL2	cis	Whole Blood	GTEx
rs4886490	ISL2	cis	multi-tissue	Pritchard
rs4886490	UBE2Q2	cis	cerebellum	SCAN
rs4886490	ISL2	cis	Lymphoblastoid	GTEx
rs4886490	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs4886490	ISL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76627000-76629000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
2	chr15:76627400-76628600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
3	chr15:76627400-76629000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
4	chr15:76627400-76629000	Bivalent Enhancer	Fetal Muscle Leg	muscle
5	chr15:76627400-76629400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr15:76627400-76629400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr15:76627400-76629600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr15:76627400-76635400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr15:76627600-76628600	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:76627600-76628600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:76627600-76628600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
12	chr15:76627600-76628600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:76627600-76628600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:76627600-76628600	Genic enhancers	Right Atrium	heart
15	chr15:76627600-76628600	Flanking Active TSS	Hela-S3	cervix
16	chr15:76627600-76628800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:76627600-76628800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
18	chr15:76627600-76628800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:76627600-76628800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:76627600-76628800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
21	chr15:76627600-76628800	Flanking Bivalent TSS/Enh	Placenta	Placenta
22	chr15:76627600-76629000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
23	chr15:76627600-76629200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr15:76627600-76629200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
25	chr15:76627600-76629400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
26	chr15:76627600-76629600	Enhancers	Pancreas	Pancrea
27	chr15:76627600-76629600	Bivalent Enhancer	Stomach Mucosa	stomach
28	chr15:76627600-76629600	Enhancers	Spleen	Spleen
29	chr15:76627600-76629800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:76627600-76630200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:76627600-76630400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
32	chr15:76627600-76630600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
33	chr15:76627600-76631000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr15:76627600-76631000	Bivalent Enhancer	Fetal Brain Male	brain
35	chr15:76627600-76631200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr15:76627600-76632400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
37	chr15:76627600-76634400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
38	chr15:76627800-76628600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
39	chr15:76627800-76628600	Bivalent Enhancer	Fetal Heart	heart
40	chr15:76627800-76628600	Enhancers	Right Ventricle	heart
41	chr15:76627800-76628600	Bivalent Enhancer	HMEC	breast
42	chr15:76627800-76628600	Flanking Bivalent TSS/Enh	NHEK	skin
43	chr15:76627800-76628800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:76627800-76629000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:76627800-76629400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
46	chr15:76627800-76629400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:76627800-76629400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
48	chr15:76627800-76629400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
49	chr15:76627800-76629800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr15:76627800-76629800	Bivalent/Poised TSS	Brain Angular Gyrus	brain

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