Variant report

Variant	rs71434254
Chromosome Location	chr15:75339054-75339055
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	PML	chr15:75338604-75340440	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:75334181-75340414	GM12878	blood:	n/a	n/a
3	IRF3	chr15:75339034-75339352	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:75338955-75339951	GM12892	blood:	n/a	n/a
5	POLR2A	chr15:75333297-75341736	GM12878	blood:	n/a	n/a
6	PAX5	chr15:75339015-75340118	GM12878	blood:	n/a	chr15:75339602-75339611
7	IKZF1	chr15:75338883-75340019	GM12878	blood:	n/a	n/a
8	BHLHE40	chr15:75339051-75339096	HepG2	liver:	n/a	n/a
9	NFIC	chr15:75338751-75340705	GM12878	blood:	n/a	chr15:75339588-75339604
10	TCF12	chr15:75339045-75340035	GM12878	blood:	n/a	n/a
11	MAX	chr15:75338937-75340297	GM12878	blood:	n/a	chr15:75339681-75339690
12	POLR2A	chr15:75338511-75340051	HL-60	blood:	n/a	n/a
13	USF2	chr15:75339023-75339139	GM12878	blood:	n/a	n/a
14	STAT5A	chr15:75338424-75340475	GM12878	blood:	n/a	chr15:75339724-75339732 chr15:75338882-75338893 chr15:75339300-75339312 chr15:75339725-75339737
15	POLR2A	chr15:75338600-75339884	GM12891	blood:	n/a	n/a
16	RUNX3	chr15:75338777-75340361	GM12878	blood:	n/a	n/a
17	ATF2	chr15:75339021-75340557	GM12878	blood:	n/a	n/a
18	POLR2A	chr15:75338409-75340378	GM12878	blood:	n/a	n/a
19	POU2F2	chr15:75339018-75340835	GM12878	blood:	n/a	n/a
20	CEBPB	chr15:75339048-75340236	GM12878	blood:	n/a	n/a
21	RUNX3	chr15:75338919-75340485	GM12878	blood:	n/a	n/a
22	POLR2A	chr15:75338823-75340239	HepG2	liver:	n/a	n/a
23	SPI1	chr15:75338622-75339118	HL-60	blood:	n/a	chr15:75338810-75338823 chr15:75338882-75338891
24	MTA3	chr15:75338784-75340743	GM12878	blood:	n/a	n/a
25	POLR2A	chr15:75338431-75340271	GM12891	blood:	n/a	n/a
26	POLR2A	chr15:75338910-75340417	GM12878	blood:	n/a	n/a
27	POLR2A	chr15:75338408-75340455	GM12892	blood:	n/a	n/a
28	FOXM1	chr15:75339008-75340310	GM12878	blood:	n/a	n/a
29	POLR2A	chr15:75338579-75340452	GM18505	blood:	n/a	n/a
30	POU2F2	chr15:75338958-75339934	GM12891	blood:	n/a	n/a
31	EBF1	chr15:75338870-75340245	GM12878	blood:	n/a	chr15:75339320-75339331
32	POLR2A	chr15:75338482-75340607	GM12878	blood:	n/a	n/a
33	ELF1	chr15:75338969-75340069	GM12878	blood:	n/a	chr15:75339598-75339611
34	POLR2A	chr15:75338759-75340265	GM12891	blood:	n/a	n/a
35	MTA3	chr15:75334888-75340698	GM12878	blood:	n/a	n/a
36	PAX5	chr15:75338923-75340031	GM12878	blood:	n/a	chr15:75339602-75339611
37	POLR2A	chr15:75338446-75340455	GM12891	blood:	n/a	n/a
38	POLR2A	chr15:75339035-75339851	GM12891	blood:	n/a	n/a
39	POLR2A	chr15:75338392-75340889	GM12892	blood:	n/a	n/a
40	POLR2A	chr15:75333262-75344076	GM12878	blood:	n/a	n/a
41	POLR2A	chr15:75338920-75340264	GM12878	blood:	n/a	n/a
42	POLR2A	chr15:75339041-75340054	GM19193	blood:	n/a	n/a
43	JUN	chr15:75338798-75340888	K562	blood:	n/a	n/a
44	STAT5A	chr15:75338894-75340395	GM12878	blood:	n/a	chr15:75339724-75339732 chr15:75339300-75339312 chr15:75339725-75339737
45	POLR2A	chr15:75338301-75340525	GM12892	blood:	n/a	n/a
46	EBF1	chr15:75338975-75340129	GM12878	blood:	n/a	chr15:75339320-75339331
47	POLR2A	chr15:75339030-75340450	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75333855..75341122-chr15:75492635..75495814,9	MCF-7	breast:
2	chr15:75318584..75321988-chr15:75334747..75339188,4	K562	blood:
3	chr15:75338159..75340815-chr15:75340871..75343132,3	MCF-7	breast:
4	chr15:75334694..75336730-chr15:75338711..75340960,2	MCF-7	breast:
5	chr15:75328843..75331250-chr15:75338652..75340222,2	MCF-7	breast:
6	chr15:75314438..75320960-chr15:75334023..75339188,6	K562	blood:
7	chr15:75337715..75339943-chr15:75401939..75403865,2	MCF-7	breast:
8	chr15:75337101..75339665-chr15:75342536..75344490,2	MCF-7	breast:
9	chr15:75331603..75340227-chr15:75492938..75499942,15	K562	blood:
10	chr15:75338739..75341398-chr15:75344086..75345973,2	MCF-7	breast:
11	chr15:75334055..75342899-chr15:75492444..75498798,20	K562	blood:
12	chr15:75337372..75339109-chr15:75499292..75501043,2	K562	blood:
13	chr15:75327523..75330367-chr15:75338576..75340222,2	MCF-7	breast:
14	chr15:75332512..75342228-chr15:75491817..75496419,22	MCF-7	breast:
15	chr15:75338171..75339673-chr15:75659821..75661787,2	K562	blood:

Variant related genes	Relation type
PPCDC	TF binding region
ENSG00000167173	Chromatin interaction
ENSG00000260483	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000140400	Chromatin interaction
ENSG00000138621	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12899456	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12902887	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12905058	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12905176	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12905302	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12906126	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12906783	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12908596	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12908919	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12910578	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12911696	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16973563	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17336944	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1822324	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2304900	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34025186	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34073905	0.81[AMR][1000 genomes]
rs34142677	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34183160	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34227381	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34268734	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34767908	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34820454	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34911644	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35056361	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35205508	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35373072	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35375675	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35396991	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35406858	0.87[AMR][1000 genomes]
rs71401669	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71401671	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71401672	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71401673	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71401675	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71401676	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71401677	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8038911	0.92[AMR][1000 genomes];0.93[EUR][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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv457205	chr15:75336729-75447773	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv569994	chr15:75336729-75447773	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75318000-75341400	Weak transcription	Brain Germinal Matrix	brain
2	chr15:75322400-75339200	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr15:75324600-75339200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr15:75328800-75350400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:75329200-75350400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:75329400-75346800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:75330600-75340000	Weak transcription	NHEK	skin
8	chr15:75333600-75341000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr15:75334000-75344600	Enhancers	Placenta	Placenta
10	chr15:75334200-75340400	Genic enhancers	Fetal Intestine Small	intestine
11	chr15:75334200-75340600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:75334200-75344600	Enhancers	Right Ventricle	heart
13	chr15:75334400-75343200	Enhancers	Fetal Heart	heart
14	chr15:75334600-75340400	Enhancers	Liver	Liver
15	chr15:75334600-75340800	Enhancers	Fetal Muscle Leg	muscle
16	chr15:75334600-75341000	Enhancers	Lung	lung
17	chr15:75334600-75343200	Enhancers	Right Atrium	heart
18	chr15:75334800-75344600	Enhancers	Left Ventricle	heart
19	chr15:75335000-75340200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr15:75335000-75340400	Enhancers	Fetal Thymus	thymus
21	chr15:75335200-75340200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:75335200-75344200	Enhancers	Fetal Lung	lung
23	chr15:75335600-75339200	Weak transcription	Fetal Kidney	kidney
24	chr15:75335600-75340400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr15:75335800-75339400	Flanking Active TSS	GM12878-XiMat	blood
26	chr15:75335800-75340600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr15:75336000-75340200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:75336000-75350400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:75336400-75339200	Weak transcription	Hela-S3	cervix
30	chr15:75336400-75340600	Enhancers	Primary hematopoietic stem cells	blood
31	chr15:75336600-75339400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr15:75336600-75340200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr15:75336600-75340600	Enhancers	Small Intestine	intestine
34	chr15:75336600-75343000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:75336800-75339200	Enhancers	Primary B cells from cord blood	blood
36	chr15:75336800-75339200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr15:75336800-75339200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr15:75336800-75339200	Enhancers	Adipose Nuclei	Adipose
39	chr15:75336800-75339200	Weak transcription	Osteobl	bone
40	chr15:75336800-75340400	Enhancers	Brain Substantia Nigra	brain
41	chr15:75336800-75340600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:75336800-75341200	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr15:75336800-75342400	Enhancers	Brain Cingulate Gyrus	brain
44	chr15:75336800-75342600	Strong transcription	Primary T cells from cord blood	blood
45	chr15:75337000-75339200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:75337000-75339200	Weak transcription	Colon Smooth Muscle	Colon
47	chr15:75337000-75339200	Weak transcription	NH-A	brain
48	chr15:75337000-75339200	Weak transcription	NHDF-Ad	bronchial
49	chr15:75337200-75339400	Weak transcription	HMEC	breast
50	chr15:75337200-75339800	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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