Variant report

Variant	rs1444940
Chromosome Location	chr15:58625121-58625122
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	chr15:58623145-58625738	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:58623397-58625260	Hela-S3	cervix:	n/a	n/a
3	SIX5	chr15:58623759-58625939	A549	lung:	n/a	chr15:58624197-58624206
4	ZNF384	chr15:58624027-58625122	K562	blood:	n/a	n/a
5	NR2F2	chr15:58624982-58625742	MCF-7	breast:	n/a	n/a
6	JUND	chr15:58623608-58625267	SK-N-SH	brain:	n/a	chr15:58624540-58624549 chr15:58624538-58624550 chr15:58624538-58624549 chr15:58624543-58624551
7	RFX5	chr15:58624155-58625329	K562	blood:	n/a	n/a
8	NR3C1	chr15:58625007-58625790	A549	lung:	n/a	chr15:58625173-58625186
9	POLR2A	chr15:58624193-58625178	GM19193	blood:	n/a	n/a
10	ATF3	chr15:58623771-58625197	K562	blood:	n/a	n/a
11	WRNIP1	chr15:58625119-58625251	GM12878	blood:	n/a	n/a
12	FOXA1	chr15:58625118-58625590	T-47D	breast:	n/a	chr15:58625409-58625424
13	TBP	chr15:58624328-58625689	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:58624046-58625222	K562	blood:	n/a	n/a
15	EP300	chr15:58625096-58625561	T-47D	breast:	n/a	chr15:58625410-58625420 chr15:58625314-58625323
16	RAD21	chr15:58624990-58625744	A549	lung:	n/a	n/a
17	JUND	chr15:58623659-58625605	K562	blood:	n/a	chr15:58624540-58624549 chr15:58625437-58625445 chr15:58625437-58625444 chr15:58624538-58624550 chr15:58624538-58624549 chr15:58624543-58624551
18	TEAD4	chr15:58623708-58625486	K562	blood:	n/a	chr15:58623903-58623912
19	ETS1	chr15:58625089-58625591	A549	lung:	n/a	chr15:58625316-58625323
20	GATA3	chr15:58624139-58625723	MCF-7	breast:	n/a	chr15:58624584-58624591
21	EP300	chr15:58623741-58626031	A549	lung:	n/a	chr15:58625410-58625420 chr15:58625314-58625323 chr15:58623911-58623925 chr15:58623868-58623882
22	TEAD4	chr15:58624042-58625792	A549	lung:	n/a	n/a
23	CEBPB	chr15:58625098-58625725	A549	lung:	n/a	n/a
24	BHLHE40	chr15:58623847-58625251	K562	blood:	n/a	n/a
25	NR3C1	chr15:58625109-58625734	A549	lung:	n/a	chr15:58625173-58625186
26	RAD21	chr15:58623989-58625691	IMR90	lung:	n/a	chr15:58624698-58624711 chr15:58624621-58624633
27	EP300	chr15:58624235-58625592	GM12878	blood:	n/a	chr15:58625410-58625420 chr15:58625314-58625323
28	FOXA2	chr15:58624029-58625769	A549	lung:	n/a	n/a
29	MAZ	chr15:58624158-58625628	HepG2	liver:	n/a	n/a
30	EBF1	chr15:58624324-58625579	GM12878	blood:	n/a	n/a
31	SP1	chr15:58623796-58625954	A549	lung:	n/a	chr15:58624213-58624227 chr15:58625601-58625608
32	CEBPB	chr15:58623524-58625784	A549	lung:	n/a	chr15:58623913-58623926
33	BRCA1	chr15:58625119-58625252	HepG2	liver:	n/a	n/a
34	TEAD4	chr15:58624876-58625430	HepG2	liver:	n/a	n/a
35	POLR2A	chr15:58624134-58625167	PBDE	blood:	n/a	n/a
36	TCF12	chr15:58624048-58625666	A549	lung:	n/a	chr15:58625411-58625420
37	TEAD4	chr15:58624938-58625617	A549	lung:	n/a	n/a
38	GATA3	chr15:58624143-58625804	A549	lung:	n/a	chr15:58624584-58624591
39	POLR2A	chr15:58623964-58625198	K562	blood:	n/a	n/a
40	SP1	chr15:58623656-58626204	A549	lung:	n/a	chr15:58624213-58624227 chr15:58625601-58625608
41	EP300	chr15:58623543-58625492	K562	blood:	n/a	chr15:58625410-58625420 chr15:58625314-58625323 chr15:58623911-58623925 chr15:58623868-58623882
42	POLR2A	chr15:58623812-58625270	MCF10A-Er-Src	breast:	n/a	n/a
43	USF1	chr15:58625087-58625618	A549	lung:	n/a	n/a
44	REST	chr15:58624851-58625685	A549	lung:	n/a	n/a
45	RAD21	chr15:58624075-58625809	A549	lung:	n/a	chr15:58624698-58624711 chr15:58624621-58624633
46	GATA3	chr15:58625097-58625554	T-47D	breast:	n/a	n/a
47	GATA2	chr15:58624137-58625177	K562	blood:	n/a	chr15:58624584-58624591
48	MAZ	chr15:58624095-58625176	GM12878	blood:	n/a	n/a
49	NR2F2	chr15:58623958-58625155	K562	blood:	n/a	n/a
50	BCL3	chr15:58623798-58625792	A549	lung:	n/a	chr15:58624221-58624230

No.	Distal block	Cell Line	Cell type
1	chr15:58588436..58590759-chr15:58624393..58625970,2	K562	blood:
2	chr15:58624616..58627086-chr15:58627284..58629454,3	MCF-7	breast:
3	chr15:58622254..58626014-chr15:59062445..59064794,4	K562	blood:
4	chr15:58624557..58626281-chr15:58684257..58686056,2	K562	blood:
5	chr15:58520576..58522119-chr15:58624457..58626342,2	K562	blood:
6	chr15:58615644..58618290-chr15:58625044..58627431,2	K562	blood:
7	chr15:58624699..58626357-chr15:58758259..58760422,2	MCF-7	breast:
8	chr15:58613929..58616800-chr15:58624666..58626264,2	MCF-7	breast:
9	chr15:58624527..58626111-chr15:58750898..58753049,2	K562	blood:
10	chr15:58621217..58623761-chr15:58624859..58627813,2	MCF-7	breast:
11	chr15:58518633..58520407-chr15:58624416..58626222,2	K562	blood:
12	chr15:58623181..58625459-chr15:58764481..58766715,2	MCF-7	breast:
13	chr15:58623889..58626326-chr15:58704441..58709164,4	K562	blood:
14	chr15:58586503..58588375-chr15:58623839..58625540,2	K562	blood:
15	chr15:58518907..58522119-chr15:58624457..58627687,4	K562	blood:
16	chr15:58624606..58626295-chr15:58688208..58690512,2	MCF-7	breast:

Variant related genes	Relation type
ALDH1A2	TF binding region
ENSG00000128923	Chromatin interaction
ENSG00000128918	Chromatin interaction
ENSG00000245975	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12905748	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16940092	0.89[CHB][hapmap]
rs1822834	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs195566	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs261281	0.90[EUR][1000 genomes]
rs35837241	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56922332	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71478664	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74015895	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047246	chr15:58375607-58707158	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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	18 gene(s)	inside rSNPs	diseases
2	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS 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	50 gene(s)	inside rSNPs	diseases
3	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats 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	50 gene(s)	inside rSNPs	diseases
4	nsv529717	chr15:58519923-58756814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv904266	chr15:58580921-58689187	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58621400-58625200	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr15:58621800-58625400	Enhancers	Primary B cells from cord blood	blood
3	chr15:58622000-58625200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr15:58622000-58625200	Enhancers	Colonic Mucosa	Colon
5	chr15:58622000-58625400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr15:58622000-58625400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr15:58622000-58625400	Enhancers	Fetal Muscle Leg	muscle
8	chr15:58622000-58625400	Enhancers	Fetal Thymus	thymus
9	chr15:58622000-58625400	Flanking Active TSS	HepG2	liver
10	chr15:58622000-58625600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:58622000-58625600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr15:58622000-58625800	Enhancers	Esophagus	oesophagus
13	chr15:58622000-58626000	Enhancers	Fetal Stomach	stomach
14	chr15:58622000-58626000	Enhancers	Left Ventricle	heart
15	chr15:58622000-58626000	Enhancers	Pancreas	Pancrea
16	chr15:58622000-58626000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr15:58622000-58626000	Enhancers	Right Atrium	heart
18	chr15:58622000-58627200	Enhancers	Placenta	Placenta
19	chr15:58622200-58625200	Enhancers	H1 Cell Line	embryonic stem cell
20	chr15:58622200-58625200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr15:58622200-58625200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr15:58622200-58625200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:58622200-58625400	Enhancers	NHEK	skin
24	chr15:58622200-58625600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:58622200-58625600	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr15:58622200-58625600	Enhancers	Stomach Mucosa	stomach
27	chr15:58622200-58625600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr15:58622200-58625800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:58622200-58625800	Enhancers	Fetal Heart	heart
30	chr15:58622200-58625800	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr15:58622200-58626000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr15:58622200-58626000	Enhancers	Fetal Intestine Large	intestine
33	chr15:58622400-58625200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:58622400-58625200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr15:58622400-58625200	Enhancers	Primary T cells fromperipheralblood	blood
36	chr15:58622400-58625400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:58622400-58625400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:58622400-58625400	Flanking Active TSS	K562	blood
39	chr15:58622400-58625800	Enhancers	Fetal Intestine Small	intestine
40	chr15:58622400-58625800	Enhancers	Psoas Muscle	Psoas
41	chr15:58622600-58625200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr15:58622600-58625200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr15:58622600-58625600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:58622600-58625600	Enhancers	Colon Smooth Muscle	Colon
45	chr15:58622600-58625800	Enhancers	Aorta	Aorta
46	chr15:58622600-58625800	Enhancers	HSMM	muscle
47	chr15:58622800-58625400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:58623000-58625400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr15:58623000-58625800	Enhancers	HMEC	breast
50	chr15:58623000-58625800	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links