Variant report

Variant	rs16972244
Chromosome Location	chr15:42210023-42210024
allele	A/C
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	POLR2A	chr15:42210000-42210545	GM12878	blood:	n/a	n/a
2	FOSL1	chr15:42209592-42210514	HCT-116	colon:	n/a	chr15:42210338-42210348 chr15:42210054-42210063 chr15:42209756-42209765 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42210338-42210348 chr15:42209755-42209765 chr15:42210053-42210064 chr15:42210338-42210348 chr15:42210054-42210064 chr15:42210055-42210064
3	MAX	chr15:42209891-42210434	A549	lung:	n/a	chr15:42210128-42210139
4	JUND	chr15:42209776-42210319	K562	blood:	n/a	chr15:42210054-42210063 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42210053-42210064 chr15:42210054-42210064 chr15:42210055-42210064
5	JUN	chr15:42209872-42210235	K562	blood:	n/a	chr15:42210054-42210063 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42210054-42210064 chr15:42210055-42210064
6	JUN	chr15:42209779-42210249	HUVEC	blood vessel:	n/a	chr15:42210054-42210063 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42210054-42210064 chr15:42210055-42210064
7	POLR2A	chr15:42209849-42210270	SK-N-SH	brain:	n/a	n/a
8	BHLHE40	chr15:42209895-42210418	K562	blood:	n/a	chr15:42210169-42210185
9	FOS	chr15:42209878-42210299	MCF10A-Er-Src	breast:	n/a	chr15:42210053-42210064 chr15:42210054-42210063 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42210054-42210064 chr15:42210055-42210064
10	MAX	chr15:42209927-42210289	K562	blood:	n/a	chr15:42210128-42210139
11	GATA2	chr15:42209879-42210202	HUVEC	blood vessel:	n/a	chr15:42210056-42210065 chr15:42210041-42210051
12	MYC	chr15:42209870-42210311	K562	blood:	n/a	chr15:42210128-42210139
13	MYC	chr15:42209933-42210311	K562	blood:	n/a	chr15:42210128-42210139
14	MAX	chr15:42209902-42210424	SK-N-SH	brain:	n/a	chr15:42210128-42210139
15	MAX	chr15:42209898-42210252	K562	blood:	n/a	chr15:42210128-42210139
16	FOS	chr15:42209667-42210270	HUVEC	blood vessel:	n/a	chr15:42210053-42210064 chr15:42210054-42210063 chr15:42209756-42209765 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42209755-42209765 chr15:42210054-42210064 chr15:42210055-42210064
17	CBX3	chr15:42209863-42210275	K562	blood:	n/a	n/a
18	FOS	chr15:42209875-42210250	K562	blood:	n/a	chr15:42210053-42210064 chr15:42210054-42210063 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42210054-42210064 chr15:42210055-42210064
19	JUN	chr15:42209837-42210304	K562	blood:	n/a	chr15:42210054-42210063 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42210054-42210064 chr15:42210055-42210064
20	ATF3	chr15:42209948-42210244	K562	blood:	n/a	n/a
21	SP1	chr15:42209732-42210485	HCT-116	colon:	n/a	chr15:42210318-42210332
22	POLR2A	chr15:42209626-42210600	GM12892	blood:	n/a	n/a
23	ATF3	chr15:42209926-42210199	K562	blood:	n/a	n/a
24	MAFF	chr15:42209930-42210156	K562	blood:	n/a	n/a
25	UBTF	chr15:42209841-42210173	K562	blood:	n/a	n/a
26	JUND	chr15:42209586-42210524	HCT-116	colon:	n/a	chr15:42210338-42210348 chr15:42210054-42210063 chr15:42209756-42209765 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42210338-42210348 chr15:42209755-42209765 chr15:42210053-42210064 chr15:42210338-42210348 chr15:42210054-42210064 chr15:42210055-42210064
27	JUND	chr15:42209669-42210479	SK-N-SH	brain:	n/a	chr15:42210338-42210348 chr15:42210054-42210063 chr15:42209756-42209765 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42210338-42210348 chr15:42209755-42209765 chr15:42210053-42210064 chr15:42210338-42210348 chr15:42210054-42210064 chr15:42210055-42210064
28	POLR2A	chr15:42209895-42210566	GM12878	blood:	n/a	n/a
29	TEAD4	chr15:42209804-42210279	K562	blood:	n/a	n/a
30	JUND	chr15:42209679-42210192	HepG2	liver:	n/a	chr15:42210054-42210063 chr15:42209756-42209765 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42209755-42209765 chr15:42210053-42210064 chr15:42210054-42210064 chr15:42210055-42210064
31	MAX	chr15:42209843-42210401	K562	blood:	n/a	chr15:42210128-42210139
32	USF1	chr15:42209980-42210254	SK-N-SH_RA	brain:	n/a	chr15:42210169-42210185
33	FOS	chr15:42209897-42210247	MCF10A-Er-Src	breast:	n/a	chr15:42210053-42210064 chr15:42210054-42210063 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42210054-42210064 chr15:42210055-42210064
34	POLR2A	chr15:42209758-42212774	GM12892	blood:	n/a	n/a
35	ATF1	chr15:42209865-42210212	K562	blood:	n/a	n/a
36	POLR2A	chr15:42209972-42210624	GM12891	blood:	n/a	n/a
37	CCNT2	chr15:42210018-42210207	K562	blood:	n/a	n/a
38	FOSL2	chr15:42209864-42210298	MCF-7	breast:	n/a	chr15:42210054-42210063 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42210054-42210064 chr15:42210055-42210064
39	TCF12	chr15:42209706-42210428	SK-N-SH	brain:	n/a	chr15:42210173-42210183
40	POLR2A	chr15:42209786-42212072	GM12878	blood:	n/a	n/a
41	EP300	chr15:42209893-42210203	K562	blood:	n/a	chr15:42210055-42210064
42	USF1	chr15:42209826-42210618	HCT-116	colon:	n/a	chr15:42210169-42210185
43	JUN	chr15:42209913-42210245	K562	blood:	n/a	chr15:42210054-42210063 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42210054-42210064 chr15:42210055-42210064
44	JUND	chr15:42209808-42210225	Hela-S3	cervix:	n/a	chr15:42210054-42210063 chr15:42210053-42210065 chr15:42210055-42210062 chr15:42210053-42210064 chr15:42210054-42210064 chr15:42210055-42210064
45	MAX	chr15:42209712-42210585	HCT-116	colon:	n/a	chr15:42209755-42209764 chr15:42210128-42210139
46	TCF12	chr15:42209650-42210465	SK-N-SH	brain:	n/a	chr15:42210173-42210183 chr15:42210447-42210456
47	MAZ	chr15:42209918-42210209	K562	blood:	n/a	chr15:42210128-42210139
48	MYC	chr15:42209954-42210308	MCF10A-Er-Src	breast:	n/a	chr15:42210128-42210139
49	E2F6	chr15:42209937-42210464	K562	blood:	n/a	chr15:42210393-42210402
50	USF1	chr15:42209971-42210251	SK-N-SH_RA	brain:	n/a	chr15:42210169-42210185

No.	Distal block	Cell Line	Cell type
1	chr15:42200852..42203519-chr15:42209900..42211491,2	K562	blood:
2	chr15:42209684..42211751-chr15:42216402..42218970,2	MCF-7	breast:
3	chr15:42207550..42209850-chr15:42209914..42212582,2	MCF-7	breast:
4	chr15:42208548..42210300-chr15:42220851..42222621,2	K562	blood:

Variant related genes	Relation type
ENSG00000259883	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1025226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1030418	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1648821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972234	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972243	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];1.00[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]
rs16972246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16972260	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs1704395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899033	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55637254	0.89[ASN][1000 genomes]
rs56008456	0.82[ASN][1000 genomes]
rs56379301	0.89[ASN][1000 genomes]
rs61753871	0.90[ASN][1000 genomes]
rs6493012	1.00[CHD][hapmap]
rs73408579	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034110	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS 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 miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
5	nsv904125	chr15:42119900-42210393	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS 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	30 gene(s)	inside rSNPs	diseases
7	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
8	nsv1054728	chr15:42177772-42310009	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv976926	chr15:42202094-42217599	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42187200-42211800	Weak transcription	Small Intestine	intestine
2	chr15:42190400-42218600	Weak transcription	Fetal Lung	lung
3	chr15:42197200-42210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:42197200-42210800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:42197200-42218600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:42197400-42218600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:42198200-42212000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:42198800-42212000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr15:42199000-42212600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr15:42201200-42225400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:42201800-42210800	Weak transcription	Thymus	Thymus
12	chr15:42201800-42211000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr15:42201800-42211600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:42202200-42210600	Weak transcription	HepG2	liver
15	chr15:42202200-42218400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr15:42202200-42218600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:42202200-42225200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:42204000-42217600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:42204200-42212000	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr15:42204400-42210800	Weak transcription	Aorta	Aorta
21	chr15:42205200-42210200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr15:42207800-42210600	Enhancers	Brain Substantia Nigra	brain
23	chr15:42208000-42210800	Genic enhancers	Adipose Nuclei	Adipose
24	chr15:42208200-42210400	Genic enhancers	HSMM	muscle
25	chr15:42208200-42210800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:42208200-42211000	Genic enhancers	HMEC	breast
27	chr15:42208200-42212000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:42208200-42212000	Strong transcription	Primary T cells from cord blood	blood
29	chr15:42208200-42212000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr15:42208200-42212000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:42208400-42210200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:42208400-42212000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:42208400-42212000	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr15:42208400-42212000	Genic enhancers	Fetal Muscle Leg	muscle
35	chr15:42208400-42212000	Genic enhancers	Lung	lung
36	chr15:42208400-42212800	Genic enhancers	Placenta	Placenta
37	chr15:42208400-42214400	Enhancers	Right Atrium	heart
38	chr15:42208400-42214800	Enhancers	Ovary	ovary
39	chr15:42208400-42218800	Genic enhancers	HUVEC	blood vessel
40	chr15:42208600-42210200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr15:42208600-42211200	Enhancers	Placenta Amnion	Placenta Amnion
42	chr15:42208600-42211800	Weak transcription	Fetal Kidney	kidney
43	chr15:42208800-42210800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:42208800-42210800	Enhancers	Right Ventricle	heart
45	chr15:42208800-42211800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:42209000-42210200	Weak transcription	Fetal Stomach	stomach
47	chr15:42209000-42210400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:42209000-42211000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr15:42209200-42210200	Weak transcription	Primary B cells from cord blood	blood
50	chr15:42209200-42210200	Enhancers	Primary hematopoietic stem cells	blood

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