Variant report

Variant	rs12594686
Chromosome Location	chr15:58624191-58624192
allele	G/T
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	EP300	chr15:58623552-58624775	Hela-S3	cervix:	n/a	chr15:58623911-58623925 chr15:58623868-58623882
3	POLR2A	chr15:58623397-58625260	Hela-S3	cervix:	n/a	n/a
4	SIX5	chr15:58623759-58625939	A549	lung:	n/a	chr15:58624197-58624206
5	ETS1	chr15:58624152-58624349	K562	blood:	n/a	chr15:58624221-58624235 chr15:58624222-58624233
6	ZNF384	chr15:58624027-58625122	K562	blood:	n/a	n/a
7	ELF1	chr15:58624119-58624396	GM12878	blood:	n/a	n/a
8	MXI1	chr15:58623871-58624791	HepG2	liver:	n/a	n/a
9	PML	chr15:58624115-58624930	GM12878	blood:	n/a	chr15:58624541-58624550
10	FOSL2	chr15:58624044-58624898	A549	lung:	n/a	chr15:58624540-58624549 chr15:58624538-58624550 chr15:58624543-58624551
11	TCF3	chr15:58624134-58624732	GM12878	blood:	n/a	n/a
12	FOXM1	chr15:58624111-58624949	ECC-1	luminal epithelium:	n/a	n/a
13	RXRA	chr15:58624123-58624781	SK-N-SH	brain:	n/a	n/a
14	MAX	chr15:58624141-58624820	GM12878	blood:	n/a	n/a
15	GATA3	chr15:58624053-58624934	MCF-7	breast:	n/a	chr15:58624584-58624591
16	TCF12	chr15:58623931-58624919	ECC-1	luminal epithelium:	n/a	n/a
17	NFIC	chr15:58623999-58624954	SK-N-SH	brain:	n/a	n/a
18	ZNF143	chr15:58624129-58624741	GM12878	blood:	n/a	n/a
19	USF1	chr15:58624003-58624962	HCT-116	colon:	n/a	n/a
20	BHLHE40	chr15:58624167-58624857	GM12878	blood:	n/a	n/a
21	GABPA	chr15:58624149-58624710	Hela-S3	cervix:	n/a	n/a
22	TCF12	chr15:58623889-58625000	SK-N-SH	brain:	n/a	n/a
23	JUND	chr15:58623608-58625267	SK-N-SH	brain:	n/a	chr15:58624540-58624549 chr15:58624538-58624550 chr15:58624538-58624549 chr15:58624543-58624551
24	ELF1	chr15:58623850-58624436	HepG2	liver:	n/a	n/a
25	MEF2A	chr15:58623913-58624730	K562	blood:	n/a	n/a
26	CREB1	chr15:58624108-58624883	HepG2	liver:	n/a	n/a
27	FOXM1	chr15:58624171-58625095	GM12878	blood:	n/a	n/a
28	RFX5	chr15:58624155-58625329	K562	blood:	n/a	n/a
29	FOSL2	chr15:58624072-58624921	SK-N-SH	brain:	n/a	chr15:58624540-58624549 chr15:58624538-58624550 chr15:58624543-58624551
30	PAX5	chr15:58624117-58624802	GM12878	blood:	n/a	chr15:58624221-58624230 chr15:58624526-58624544 chr15:58624528-58624545 chr15:58624535-58624544
31	ATF3	chr15:58623771-58625197	K562	blood:	n/a	n/a
32	FOS	chr15:58623732-58624761	MCF10A-Er-Src	breast:	n/a	chr15:58624540-58624549 chr15:58624538-58624550 chr15:58624538-58624549 chr15:58624543-58624551
33	TCF7L2	chr15:58624040-58624754	HCT-116	colon:	n/a	chr15:58624540-58624549
34	NR3C1	chr15:58624191-58624826	A549	lung:	n/a	chr15:58624688-58624701 chr15:58624540-58624549
35	ELK1	chr15:58623690-58624834	Hela-S3	cervix:	n/a	n/a
36	CEBPB	chr15:58622930-58625028	Hela-S3	cervix:	n/a	chr15:58623913-58623926
37	POLR2A	chr15:58624046-58625222	K562	blood:	n/a	n/a
38	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
39	TEAD4	chr15:58623708-58625486	K562	blood:	n/a	chr15:58623903-58623912
40	ZBTB33	chr15:58624049-58624856	A549	lung:	n/a	n/a
41	USF2	chr15:58623172-58625082	Hela-S3	cervix:	n/a	n/a
42	NFIC	chr15:58623878-58624857	GM12878	blood:	n/a	n/a
43	POLR2A	chr15:58623950-58624914	Hela-S3	cervix:	n/a	n/a
44	STAT3	chr15:58624080-58624726	MCF10A-Er-Src	breast:	n/a	n/a
45	USF1	chr15:58624096-58624825	K562	blood:	n/a	n/a
46	GATA3	chr15:58624139-58625723	MCF-7	breast:	n/a	chr15:58624584-58624591
47	SRF	chr15:58624178-58624778	ECC-1	luminal epithelium:	n/a	n/a
48	SIN3A	chr15:58624154-58624770	H1-hESC	embryonic stem cell:	n/a	chr15:58624472-58624486
49	FOSL2	chr15:58624068-58624817	HepG2	liver:	n/a	chr15:58624540-58624549 chr15:58624538-58624550 chr15:58624543-58624551
50	MAZ	chr15:58623137-58624773	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:58622254..58626014-chr15:59062445..59064794,4	K562	blood:
2	chr15:58623181..58625459-chr15:58764481..58766715,2	MCF-7	breast:
3	chr15:58623889..58626326-chr15:58704441..58709164,4	K562	blood:
4	chr15:58586503..58588375-chr15:58623839..58625540,2	K562	blood:

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

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12594224	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs1652518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1652520	0.92[ASN][1000 genomes]
rs1663238	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56996176	0.81[ASN][1000 genomes]
rs8032466	1.00[CEU][hapmap]
rs8032700	1.00[CEU][hapmap]
rs8033458	1.00[CEU][hapmap]
rs8039902	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv522166	chr15:58623408-58624328	Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58621200-58624800	Enhancers	Primary T cells from cord blood	blood
2	chr15:58621400-58624200	Flanking Active TSS	Liver	Liver
3	chr15:58621400-58625200	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr15:58621800-58624400	Enhancers	Fetal Kidney	kidney
5	chr15:58621800-58625400	Enhancers	Primary B cells from cord blood	blood
6	chr15:58622000-58624200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr15:58622000-58624400	Flanking Active TSS	Hela-S3	cervix
8	chr15:58622000-58624600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr15:58622000-58624600	Enhancers	Thymus	Thymus
10	chr15:58622000-58625000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr15:58622000-58625200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr15:58622000-58625200	Enhancers	Colonic Mucosa	Colon
13	chr15:58622000-58625400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr15:58622000-58625400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr15:58622000-58625400	Enhancers	Fetal Muscle Leg	muscle
16	chr15:58622000-58625400	Enhancers	Fetal Thymus	thymus
17	chr15:58622000-58625400	Flanking Active TSS	HepG2	liver
18	chr15:58622000-58625600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:58622000-58625600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr15:58622000-58625800	Enhancers	Esophagus	oesophagus
21	chr15:58622000-58626000	Enhancers	Fetal Stomach	stomach
22	chr15:58622000-58626000	Enhancers	Left Ventricle	heart
23	chr15:58622000-58626000	Enhancers	Pancreas	Pancrea
24	chr15:58622000-58626000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr15:58622000-58626000	Enhancers	Right Atrium	heart
26	chr15:58622000-58627200	Enhancers	Placenta	Placenta
27	chr15:58622200-58624600	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr15:58622200-58625200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr15:58622200-58625200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr15:58622200-58625200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr15:58622200-58625200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:58622200-58625400	Enhancers	NHEK	skin
33	chr15:58622200-58625600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:58622200-58625600	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr15:58622200-58625600	Enhancers	Stomach Mucosa	stomach
36	chr15:58622200-58625600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr15:58622200-58625800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:58622200-58625800	Enhancers	Fetal Heart	heart
39	chr15:58622200-58625800	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr15:58622200-58626000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr15:58622200-58626000	Enhancers	Fetal Intestine Large	intestine
42	chr15:58622400-58624200	Enhancers	HSMMtube	muscle
43	chr15:58622400-58624800	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr15:58622400-58625000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:58622400-58625000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr15:58622400-58625200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:58622400-58625200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:58622400-58625200	Enhancers	Primary T cells fromperipheralblood	blood
49	chr15:58622400-58625400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr15:58622400-58625400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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