Variant report

Variant	rs10872886
Chromosome Location	chr14:21574690-21574691
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	TEAD4	chr14:21574408-21575674	HepG2	liver:	n/a	n/a
2	RFX5	chr14:21574675-21575332	HepG2	liver:	n/a	chr14:21574818-21574826
3	EP300	chr14:21574284-21575450	A549	lung:	n/a	chr14:21574452-21574466
4	TCF7L2	chr14:21574587-21575927	Hela-S3	cervix:	n/a	n/a
5	CUX1	chr14:21574631-21574840	GM12878	blood:	n/a	n/a
6	EP300	chr14:21574350-21575200	Hela-S3	cervix:	n/a	chr14:21574452-21574466
7	CTCF	chr14:21573742-21575975	A549	lung:	n/a	chr14:21575181-21575202 chr14:21575186-21575204 chr14:21575188-21575201
8	MAFK	chr14:21574651-21575191	HepG2	liver:	n/a	chr14:21574898-21574915
9	JUND	chr14:21574564-21575368	HepG2	liver:	n/a	chr14:21574902-21574911
10	FOS	chr14:21574336-21574815	MCF10A-Er-Src	breast:	n/a	n/a
11	E2F4	chr14:21574382-21574703	MCF10A-Er-Src	breast:	n/a	n/a
12	CTCF	chr14:21574418-21575881	SK-N-SH	brain:	n/a	chr14:21575181-21575202 chr14:21575186-21575204 chr14:21575188-21575201
13	CEBPB	chr14:21574385-21575238	A549	lung:	n/a	chr14:21574730-21574747
14	RCOR1	chr14:21574674-21575383	HepG2	liver:	n/a	n/a
15	FOS	chr14:21574334-21574693	MCF10A-Er-Src	breast:	n/a	n/a
16	CEBPB	chr14:21574315-21575920	Hela-S3	cervix:	n/a	chr14:21574730-21574747
17	STAT1	chr14:21574504-21576101	Hela-S3	cervix:	n/a	chr14:21575783-21575794 chr14:21575914-21575922
18	YY1	chr14:21574374-21575390	HepG2	liver:	n/a	chr14:21575142-21575161 chr14:21575186-21575198 chr14:21575137-21575159 chr14:21575148-21575156 chr14:21575147-21575159
19	NFIC	chr14:21574544-21575535	HepG2	liver:	n/a	n/a
20	SMC3	chr14:21574416-21575962	Hela-S3	cervix:	n/a	chr14:21575188-21575202 chr14:21575390-21575400 chr14:21575404-21575414 chr14:21575178-21575192 chr14:21575407-21575415
21	STAT3	chr14:21574335-21574858	MCF10A-Er-Src	breast:	n/a	chr14:21574785-21574796
22	SMARCC1	chr14:21574344-21575888	Hela-S3	cervix:	n/a	chr14:21575771-21575780
23	GTF2F1	chr14:21574485-21575961	Hela-S3	cervix:	n/a	n/a
24	FOSL2	chr14:21574236-21574850	A549	lung:	n/a	n/a
25	MYBL2	chr14:21574450-21575432	HepG2	liver:	n/a	n/a
26	MAFF	chr14:21574609-21575327	HepG2	liver:	n/a	n/a
27	FOS	chr14:21574368-21574719	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr14:21574414-21575305	MCF10A-Er-Src	breast:	n/a	chr14:21574785-21574796
29	MAFK	chr14:21574501-21575829	Hela-S3	cervix:	n/a	chr14:21574898-21574915
30	MAZ	chr14:21574622-21574822	Hela-S3	cervix:	n/a	n/a
31	STAT3	chr14:21574341-21575152	MCF10A-Er-Src	breast:	n/a	chr14:21574785-21574796
32	NR3C1	chr14:21574388-21574729	A549	lung:	n/a	n/a
33	MAX	chr14:21574451-21575985	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr14:21574620-21574770	SAEC	small airway:	n/a	n/a
35	SMC3	chr14:21574665-21575409	HepG2	liver:	n/a	chr14:21575188-21575202 chr14:21575390-21575400 chr14:21575178-21575192
36	CEBPB	chr14:21574386-21575212	IMR90	lung:	n/a	chr14:21574730-21574747
37	STAT3	chr14:21574368-21575225	MCF10A-Er-Src	breast:	n/a	chr14:21574785-21574796
38	KAP1	chr14:21574576-21575510	HEK293	kidney:	n/a	n/a
39	RAD21	chr14:21574437-21575620	SK-N-SH	brain:	n/a	chr14:21575190-21575199 chr14:21575335-21575348 chr14:21574663-21574675 chr14:21575188-21575202 chr14:21575187-21575200 chr14:21575184-21575203
40	TFAP2C	chr14:21574306-21575909	Hela-S3	cervix:	n/a	n/a
41	CEBPB	chr14:21574257-21574807	A549	lung:	n/a	chr14:21574730-21574747
42	POLR2A	chr14:21574469-21574812	Hela-S3	cervix:	n/a	n/a
43	SP1	chr14:21574247-21574810	A549	lung:	n/a	n/a
44	FOS	chr14:21574337-21574782	MCF10A-Er-Src	breast:	n/a	n/a
45	CEBPB	chr14:21574431-21575250	HepG2	liver:	n/a	chr14:21574730-21574747
46	MYC	chr14:21574337-21574708	MCF10A-Er-Src	breast:	n/a	n/a
47	RCOR1	chr14:21574447-21575956	Hela-S3	cervix:	n/a	n/a
48	CHD2	chr14:21574348-21574786	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr14:21574460-21574769	Hela-S3	cervix:	n/a	n/a
50	ZKSCAN1	chr14:21574445-21574809	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr14:21574644-21574694	H1-hESC	embryonic stem cell:	embryo
2	chr14:21574644-21574694	HNPCEpiC	eye:	n/a
3	chr14:21574644-21574694	HL-60	blood:	n/a
4	chr14:21574644-21574694	MCF10A-Er-Src	breast:	n/a
5	chr14:21574644-21574694	PFSK-1	brain:	n/a
6	chr14:21574644-21574694	AoSMC	blood vessel:	n/a
7	chr14:21574644-21574694	AG04449	skin:	fetal
8	chr14:21574644-21574694	MCF-7	breast:	n/a
9	chr14:21574644-21574694	HRE	kidney:	n/a
10	chr14:21574644-21574694	NT2-D1	testis:	n/a
11	chr14:21574644-21574694	AG04450	lung:	fetal
12	chr14:21574644-21574694	HUVEC	blood vessel:	n/a
13	chr14:21574644-21574694	SK-N-SH_RA	brain:	n/a
14	chr14:21574644-21574694	HCT-116	colon:	n/a
15	chr14:21574644-21574694	A549	lung:	n/a
16	chr14:21574644-21574694	AG10803	skin:	n/a
17	chr14:21574644-21574694	T-47D	breast:	n/a
18	chr14:21574644-21574694	AG09309	skin:	n/a
19	chr14:21574644-21574694	HepG2	liver:	n/a
20	chr14:21574644-21574694	GM12891	blood:	n/a
21	chr14:21574644-21574694	IMR90	lung:	fetal
22	chr14:21574644-21574694	HRPEpiC	eye:	n/a
23	chr14:21574644-21574694	HEEpiC	esophagus:	n/a
24	chr14:21574644-21574694	NB4	blood:	n/a
25	chr14:21574644-21574694	Caco-2	colon:	n/a
26	chr14:21574644-21574694	BJ	skin:	n/a
27	chr14:21574644-21574694	HMEC	breast:	n/a
28	chr14:21574644-21574694	PrEC	prostate:	n/a
29	chr14:21574644-21574694	K562	blood:	n/a
30	chr14:21574644-21574694	HRCEpiC	kidney:	n/a
31	chr14:21574644-21574694	LNCaP	prostate:	n/a
32	chr14:21574644-21574694	ovcar-3	ovarian:	n/a
33	chr14:21574644-21574694	HPAEpiC	pulmonary alveolar:	n/a
34	chr14:21574644-21574694	HCM	heart:	n/a
35	chr14:21574644-21574694	ProgFib	skin:	n/a
36	chr14:21574644-21574694	PANC-1	pancreas:	n/a
37	chr14:21574644-21574694	NH-A	brain:	n/a
38	chr14:21574644-21574694	GM12892	blood:	n/a
39	chr14:21574644-21574694	Jurkat	blood:	n/a
40	chr14:21574644-21574694	GM12878	blood:	n/a
41	chr14:21574644-21574694	ECC-1	luminal epithelium:	n/a
42	chr14:21574644-21574694	NHBE	bronchial:	n/a
43	chr14:21574644-21574694	HCF	heart:	n/a
44	chr14:21574644-21574694	U87	brain:	n/a
45	chr14:21574644-21574694	SK-N-SH	brain:	n/a
46	chr14:21574644-21574694	HEK293	kidney:	embryo
47	chr14:21574644-21574694	GM19239	blood:	n/a
48	chr14:21574644-21574694	GM06990	blood:	n/a
49	chr14:21574644-21574694	NHDF-neo	bronchial:	n/a
50	chr14:21574644-21574694	HAEpiC	amniotic membrane:	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:21482752..21484082-chr14:21574253..21575653,5	MCF-7	breast:
2	chr14:21560382..21561252-chr14:21574427..21575723,4	K562	blood:
3	chr14:21536374..21537276-chr14:21574658..21575637,5	MCF-7	breast:
4	chr14:21482544..21483098-chr14:21574679..21575685,3	K562	blood:
5	chr14:21535299..21541334-chr14:21568487..21576770,16	MCF-7	breast:
6	chr14:21560181..21561638-chr14:21574686..21576156,8	MCF-7	breast:
7	chr14:21535250..21540469-chr14:21570413..21576715,8	K562	blood:
8	chr14:21572213..21574693-chr17:56708000..56709846,2	MCF-7	breast:
9	chr14:21535130..21541812-chr14:21564802..21576767,22	MCF-7	breast:
10	chr14:21482503..21483435-chr14:21574421..21575440,4	MCF-7	breast:
11	chr14:21535951..21540860-chr14:21573309..21578466,6	K562	blood:

Variant related genes	Relation type
ZNF219	TF binding region
ENSG00000178107	TF binding region
ZNF219	CpG island
ENSG00000178107	CpG island
ENSG00000212195	Chromatin interaction
ENSG00000165795	Chromatin interaction
ENSG00000165801	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10141637	0.87[ASN][1000 genomes]
rs11156853	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11628703	0.82[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12893688	0.82[CHD][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap];0.81[ASN][1000 genomes]
rs4982408	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8010018	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8021387	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[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	nsv530009	chr14:21377022-22044608	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
2	nsv530769	chr14:21407536-22139126	Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv916319	chr14:21507092-21896590	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1036762	chr14:21507093-22101805	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats 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	92 gene(s)	inside rSNPs	diseases
5	nsv541976	chr14:21507093-22101805	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv826882	chr14:21511021-21604201	Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv530770	chr14:21526410-21852363	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
8	nsv525724	chr14:21540863-21574690	Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv524093	chr14:21574690-21652897	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10872886	PRMT5	cis	cerebellum	SCAN
rs10872886	RNASE6	cis	lymphoblastoid	seeQTL
rs10872886	OR6S1	cis	cerebellum	SCAN
rs10872886	OR4K14	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21572400-21575400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr14:21572800-21576400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr14:21573000-21574800	Enhancers	Primary B cells from cord blood	blood
4	chr14:21573000-21574800	Weak transcription	HSMMtube	muscle
5	chr14:21573000-21575600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr14:21573000-21575800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr14:21573000-21575800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr14:21573000-21576200	Enhancers	Fetal Muscle Trunk	muscle
9	chr14:21573000-21576400	Enhancers	NHEK	skin
10	chr14:21573200-21574800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr14:21573200-21574800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr14:21573200-21575800	Enhancers	Fetal Intestine Small	intestine
13	chr14:21573200-21576400	Enhancers	Fetal Intestine Large	intestine
14	chr14:21573200-21576400	Enhancers	HMEC	breast
15	chr14:21573200-21576800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr14:21573400-21574800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr14:21573400-21574800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr14:21573400-21574800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr14:21573400-21574800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr14:21573400-21575000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr14:21573400-21575600	Enhancers	Fetal Lung	lung
22	chr14:21573400-21576200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr14:21573400-21576400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr14:21573600-21574800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr14:21573800-21574800	Weak transcription	Stomach Mucosa	stomach
26	chr14:21574000-21575000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr14:21574000-21575200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr14:21574200-21574800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr14:21574200-21574800	Enhancers	Small Intestine	intestine
30	chr14:21574200-21575000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr14:21574200-21575200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr14:21574200-21575200	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr14:21574200-21575400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr14:21574200-21575400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr14:21574200-21575800	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr14:21574200-21575800	Enhancers	Fetal Muscle Leg	muscle
37	chr14:21574200-21575800	Flanking Active TSS	HepG2	liver
38	chr14:21574200-21576400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr14:21574400-21574800	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr14:21574400-21574800	Enhancers	Fetal Kidney	kidney
41	chr14:21574400-21574800	Enhancers	NH-A	brain
42	chr14:21574400-21575200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr14:21574400-21575200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr14:21574400-21575400	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr14:21574400-21575400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr14:21574400-21575400	Enhancers	Dnd41	blood
47	chr14:21574400-21575600	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr14:21574400-21575600	Enhancers	Stomach Smooth Muscle	stomach
49	chr14:21574400-21575600	Flanking Active TSS	A549	lung
50	chr14:21574400-21575600	Flanking Active TSS	Osteobl	bone

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