Variant report

Variant	rs6493032
Chromosome Location	chr15:42565942-42565943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:363)
CpG islands
(count:61)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:363 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBP	chr15:42565096-42567024	K562	blood:	n/a	n/a
2	FOXA1	chr15:42565451-42566001	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:42565017-42566795	GM12892	blood:	n/a	n/a
4	POLR2A	chr15:42565014-42566618	GM12891	blood:	n/a	n/a
5	GABPA	chr15:42565122-42565993	HL-60	blood:	n/a	chr15:42565779-42565793 chr15:42565782-42565791
6	POLR2A	chr15:42565039-42566853	HepG2	liver:	n/a	n/a
7	TAF1	chr15:42565004-42566525	Hela-S3	cervix:	n/a	n/a
8	E2F4	chr15:42565162-42566167	K562	blood:	n/a	chr15:42565783-42565792
9	TCF12	chr15:42564971-42565985	ECC-1	luminal epithelium:	n/a	n/a
10	TAF1	chr15:42565062-42566103	H1-hESC	embryonic stem cell:	n/a	n/a
11	MTA3	chr15:42564945-42567034	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:42564953-42566886	HUVEC	blood vessel:	n/a	n/a
13	KAP1	chr15:42564749-42566769	HEK293	kidney:	n/a	chr15:42566671-42566679
14	POLR2A	chr15:42565173-42566064	HUVEC	blood vessel:	n/a	n/a
15	MYC	chr15:42565122-42567080	K562	blood:	n/a	n/a
16	FOXA2	chr15:42565380-42566073	A549	lung:	n/a	n/a
17	GTF2F1	chr15:42565264-42566030	H1-hESC	embryonic stem cell:	n/a	n/a
18	JUND	chr15:42565003-42566846	K562	blood:	n/a	n/a
19	POLR2A	chr15:42565014-42566687	HUVEC	blood vessel:	n/a	n/a
20	ZMIZ1	chr15:42565295-42566273	K562	blood:	n/a	n/a
21	POLR2A	chr15:42565130-42566806	HL-60	blood:	n/a	n/a
22	MAX	chr15:42565149-42566578	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr15:42565161-42566041	HCT-116	colon:	n/a	n/a
24	SP1	chr15:42565098-42565974	A549	lung:	n/a	chr15:42565342-42565353 chr15:42565647-42565661 chr15:42565401-42565413 chr15:42565343-42565353 chr15:42565402-42565412 chr15:42565402-42565411
25	SIN3A	chr15:42564930-42566420	H1-hESC	embryonic stem cell:	n/a	n/a
26	GABPA	chr15:42565119-42566084	HL-60	blood:	n/a	chr15:42565779-42565793 chr15:42565782-42565791
27	RAD21	chr15:42565591-42565994	HepG2	liver:	n/a	n/a
28	WRNIP1	chr15:42564953-42567418	GM12878	blood:	n/a	n/a
29	POLR2A	chr15:42565233-42566129	MCF-7	breast:	n/a	n/a
30	YY1	chr15:42565104-42566795	GM12878	blood:	n/a	chr15:42565586-42565606
31	EP300	chr15:42565194-42566227	HepG2	liver:	n/a	chr15:42565713-42565723
32	POLR2A	chr15:42565106-42566522	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr15:42565033-42566453	HCT-116	colon:	n/a	n/a
34	POLR2A	chr15:42564877-42566879	SK-N-MC	brain:	n/a	n/a
35	CHD2	chr15:42565086-42566537	GM12878	blood:	n/a	chr15:42565927-42565937
36	SMC3	chr15:42565168-42566008	GM12878	blood:	n/a	n/a
37	ELF1	chr15:42565119-42566078	K562	blood:	n/a	chr15:42565634-42565647
38	GTF2B	chr15:42565231-42566439	K562	blood:	n/a	n/a
39	HNF4G	chr15:42565497-42565950	HepG2	liver:	n/a	chr15:42565764-42565779 chr15:42565764-42565779
40	POLR2A	chr15:42565063-42566221	H1-neurons	neurons:	n/a	n/a
41	E2F6	chr15:42565268-42565981	A549	lung:	n/a	chr15:42565783-42565792
42	BRCA1	chr15:42564758-42566829	Hela-S3	cervix:	n/a	chr15:42565231-42565238
43	MXI1	chr15:42565126-42566743	HepG2	liver:	n/a	n/a
44	TAF1	chr15:42565036-42566251	ECC-1	luminal epithelium:	n/a	n/a
45	TAF1	chr15:42565301-42565956	GM12891	blood:	n/a	n/a
46	RFX5	chr15:42564973-42566898	Hela-S3	cervix:	n/a	n/a
47	RCOR1	chr15:42565075-42567038	K562	blood:	n/a	n/a
48	MYC	chr15:42565220-42566789	K562	blood:	n/a	n/a
49	POLR2A	chr15:42565059-42566803	GM18505	blood:	n/a	n/a
50	MYC	chr15:42565108-42566606	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:42565903-42565953	PANC-1	pancreas:	n/a
2	chr15:42565903-42565953	BE2_C	brain:	n/a
3	chr15:42565903-42565953	AG10803	skin:	n/a
4	chr15:42565903-42565953	NB4	blood:	n/a
5	chr15:42565903-42565953	AoSMC	blood vessel:	n/a
6	chr15:42565903-42565953	GM19239	blood:	n/a
7	chr15:42565903-42565953	HMEC	breast:	n/a
8	chr15:42565903-42565953	GM12878	blood:	n/a
9	chr15:42565903-42565953	MCF10A-Er-Src	breast:	n/a
10	chr15:42565903-42565953	HPAEpiC	pulmonary alveolar:	n/a
11	chr15:42565903-42565953	HNPCEpiC	eye:	n/a
12	chr15:42565903-42565953	NHDF-neo	bronchial:	n/a
13	chr15:42565903-42565953	SK-N-MC	brain:	n/a
14	chr15:42565903-42565953	HRPEpiC	eye:	n/a
15	chr15:42565903-42565953	NHBE	bronchial:	n/a
16	chr15:42565903-42565953	AG04450	lung:	fetal
17	chr15:42565903-42565953	AG09309	skin:	n/a
18	chr15:42565903-42565953	AG04449	skin:	fetal
19	chr15:42565903-42565953	Hepatocyte	liver:	n/a
20	chr15:42565903-42565953	BJ	skin:	n/a
21	chr15:42565903-42565953	HRE	kidney:	n/a
22	chr15:42565903-42565953	HCM	heart:	n/a
23	chr15:42565903-42565953	HepG2	liver:	n/a
24	chr15:42565903-42565953	T-47D	breast:	n/a
25	chr15:42565903-42565953	SK-N-SH	brain:	n/a
26	chr15:42565903-42565953	H1-hESC	embryonic stem cell:	embryo
27	chr15:42565903-42565953	K562	blood:	n/a
28	chr15:42565903-42565953	HUVEC	blood vessel:	n/a
29	chr15:42565903-42565953	SAEC	small airway:	n/a
30	chr15:42565903-42565953	MCF-7	breast:	n/a
31	chr15:42565903-42565953	ProgFib	skin:	n/a
32	chr15:42565903-42565953	Hela-S3	cervix:	n/a
33	chr15:42565903-42565953	RPTEC	kidney:	n/a
34	chr15:42565903-42565953	HRCEpiC	kidney:	n/a
35	chr15:42565903-42565953	IMR90	lung:	fetal
36	chr15:42565903-42565953	U87	brain:	n/a
37	chr15:42565903-42565953	Caco-2	colon:	n/a
38	chr15:42565903-42565953	HCT-116	colon:	n/a
39	chr15:42565903-42565953	LNCaP	prostate:	n/a
40	chr15:42565903-42565953	HAEpiC	amniotic membrane:	n/a
41	chr15:42565903-42565953	CMK	blood:	n/a
42	chr15:42565903-42565953	ECC-1	luminal epithelium:	n/a
43	chr15:42565903-42565953	HEEpiC	esophagus:	n/a
44	chr15:42565903-42565953	HL-60	blood:	n/a
45	chr15:42565903-42565953	ovcar-3	ovarian:	n/a
46	chr15:42565903-42565953	PFSK-1	brain:	n/a
47	chr15:42565903-42565953	HCPEpiC	choroid plexus:	n/a
48	chr15:42565903-42565953	GM12892	blood:	n/a
49	chr15:42565903-42565953	NT2-D1	testis:	n/a
50	chr15:42565903-42565953	GM06990	blood:	n/a

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:42565172..42565968-chr3:20227231..20227766,2	Hela-S3	cervix:
2	chr15:42565208..42566147-chr19:48824795..48825577,2	NB4	blood:
3	chr11:34073237..34073837-chr15:42565350..42566240,2	Hela-S3	cervix:
4	chr15:42453296..42455922-chr15:42565346..42568176,2	K562	blood:
5	chr11:71814032..71814862-chr15:42565436..42566128,2	NB4	blood:
6	chr15:42565726..42566604-chr15:65588308..65589204,2	Hela-S3	cervix:
7	chr15:42565452..42566007-chr6:13328640..13329262,2	Hela-S3	cervix:
8	chr15:42565173..42566146-chr19:17829994..17830507,2	HCT-116	colon:
9	chr1:147806312..147807083-chr15:42565139..42566022,2	Hela-S3	cervix:
10	chr15:42564636..42566534-chr15:42781561..42783413,2	K562	blood:
11	chr13:96328903..96329487-chr15:42565285..42566134,2	Hela-S3	cervix:
12	chr15:42565177..42566160-chr3:69062410..69063138,2	Hela-S3	cervix:
13	chr11:62554539..62555349-chr15:42565272..42566248,2	Hela-S3	cervix:
14	chr15:42565305..42567163-chr15:42839364..42842481,3	K562	blood:
15	chr15:42498938..42502268-chr15:42564432..42567193,3	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM87A	TF binding region
GANC	TF binding region
TMEM87A	CpG island
GANC	CpG island
ENSG00000129810	Chromatin interaction
ENSG00000180979	Chromatin interaction
ENSG00000149357	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000163378	Chromatin interaction
ENSG00000261002	Chromatin interaction
ENSG00000103994	Chromatin interaction
ENSG00000247400	Chromatin interaction
ENSG00000105479	Chromatin interaction
ENSG00000202408	Chromatin interaction
ENSG00000102580	Chromatin interaction
ENSG00000185475	Chromatin interaction
ENSG00000145979	Chromatin interaction
ENSG00000130479	Chromatin interaction
ENSG00000244513	Chromatin interaction
ENSG00000135387	Chromatin interaction
ENSG00000137814	Chromatin interaction
ENSG00000166887	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16972704	1.00[EUR][1000 genomes]
rs16972772	1.00[EUR][1000 genomes]
rs16972775	1.00[EUR][1000 genomes]
rs16972973	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16972983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16972993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973103	1.00[EUR][1000 genomes]
rs16973149	1.00[EUR][1000 genomes]
rs16973183	1.00[EUR][1000 genomes]
rs16973203	1.00[EUR][1000 genomes]
rs16973233	1.00[EUR][1000 genomes]
rs28364353	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364361	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364362	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364364	1.00[ASW][hapmap];1.00[MKK][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364366	1.00[AMR][1000 genomes]
rs28364375	1.00[EUR][1000 genomes]
rs28364412	1.00[EUR][1000 genomes]
rs28364442	1.00[EUR][1000 genomes]
rs28364445	1.00[EUR][1000 genomes]
rs28364450	1.00[EUR][1000 genomes]
rs28364499	1.00[ASW][hapmap];1.00[EUR][1000 genomes]
rs59897576	1.00[EUR][1000 genomes]
rs61735534	1.00[EUR][1000 genomes]
rs7163294	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7164282	1.00[EUR][1000 genomes]
rs7183741	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8026177	1.00[EUR][1000 genomes]
rs8031541	1.00[EUR][1000 genomes]
rs8037390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8037485	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8037624	1.00[EUR][1000 genomes]
rs8041155	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042890	1.00[AMR][1000 genomes]
rs9672364	1.00[EUR][1000 genomes]
rs9745221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	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	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
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	esv1807328	chr15:42525300-42573278	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	nsv827310	chr15:42565606-42566319	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42562800-42566600	Active TSS	NHLF	lung
2	chr15:42563000-42566800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:42563000-42566800	Active TSS	Fetal Intestine Large	intestine
4	chr15:42563200-42567400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr15:42563400-42566400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:42563400-42566600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:42563400-42568200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:42563400-42568600	Active TSS	Right Atrium	heart
9	chr15:42563600-42566800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:42563600-42566800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:42563800-42566600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:42563800-42566600	Active TSS	HMEC	breast
13	chr15:42563800-42567000	Active TSS	GM12878-XiMat	blood
14	chr15:42564000-42566400	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr15:42564000-42566600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:42564000-42566600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:42564000-42566600	Active TSS	Brain Germinal Matrix	brain
18	chr15:42564000-42566600	Active TSS	NHEK	skin
19	chr15:42564000-42566800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:42564000-42566800	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr15:42564000-42566800	Active TSS	NHDF-Ad	bronchial
22	chr15:42564000-42567000	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr15:42564000-42567200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:42564000-42567600	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr15:42564000-42568400	Active TSS	K562	blood
26	chr15:42564200-42566600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:42564200-42566800	Active TSS	Fetal Kidney	kidney
28	chr15:42564200-42567000	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr15:42564200-42567000	Active TSS	A549	lung
30	chr15:42564400-42566000	Active TSS	Fetal Muscle Leg	muscle
31	chr15:42564400-42566800	Active TSS	H1 Cell Line	embryonic stem cell
32	chr15:42564400-42566800	Active TSS	HSMM	muscle
33	chr15:42564400-42566800	Active TSS	HSMMtube	muscle
34	chr15:42564400-42567000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:42564400-42567800	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr15:42564400-42568400	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr15:42564400-42568400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:42564600-42566000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr15:42564600-42566200	ZNF genes & repeats	Fetal Brain Male	brain
40	chr15:42564600-42566400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:42564600-42566600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr15:42564600-42566600	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr15:42564600-42566600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:42564600-42566600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:42564600-42566600	Active TSS	Primary T cells fromperipheralblood	blood
46	chr15:42564600-42566600	Active TSS	Fetal Lung	lung
47	chr15:42564600-42566600	Active TSS	Fetal Stomach	stomach
48	chr15:42564600-42566600	Active TSS	Placenta Amnion	Placenta Amnion
49	chr15:42564600-42566800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr15:42564600-42566800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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