Variant report

Variant	rs3742520
Chromosome Location	chr14:24901249-24901250
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:243)
CpG islands
(count:0)
Chromatin interactive
region (count:34)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:243 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:24901020-24901627	GM12891	blood:	n/a	n/a
2	POLR2A	chr14:24900660-24903180	HepG2	liver:	n/a	n/a
3	CTCF	chr14:24901100-24901250	RPTEC	kidney:	n/a	n/a
4	TCF12	chr14:24900808-24901434	A549	lung:	n/a	n/a
5	RFX5	chr14:24900938-24901282	Hela-S3	cervix:	n/a	n/a
6	TCF12	chr14:24900960-24901270	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr14:24900948-24901321	MCF-7	breast:	n/a	n/a
8	POLR2A	chr14:24900988-24901323	K562	blood:	n/a	n/a
9	CTCF	chr14:24900959-24901292	Medullo	brain:	n/a	n/a
10	CTCF	chr14:24900944-24901474	MCF-7	breast:	n/a	n/a
11	CTCF	chr14:24901100-24901250	HEK293	kidney:	n/a	n/a
12	RAD21	chr14:24900942-24901323	K562	blood:	n/a	n/a
13	RAD21	chr14:24900795-24901548	HCT-116	colon:	n/a	n/a
14	POLR2A	chr14:24900874-24901322	K562	blood:	n/a	n/a
15	ATF2	chr14:24900825-24901340	GM12878	blood:	n/a	n/a
16	CTCF	chr14:24900921-24901341	GM12878	blood:	n/a	n/a
17	MAZ	chr14:24900903-24901358	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr14:24900831-24901706	HCT-116	colon:	n/a	n/a
19	ZNF143	chr14:24900867-24901327	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr14:24900976-24901298	GM10266	blood:	n/a	n/a
21	POLR2A	chr14:24900936-24901254	U87	brain:	n/a	n/a
22	POLR2A	chr14:24900821-24901296	Raji	blood:	n/a	n/a
23	RAD21	chr14:24900926-24901319	SK-N-SH_RA	brain:	n/a	n/a
24	RCOR1	chr14:24900910-24901310	HepG2	liver:	n/a	n/a
25	MAZ	chr14:24898402-24901483	IMR90	lung:	n/a	chr14:24898793-24898803
26	MAFK	chr14:24901012-24901324	K562	blood:	n/a	n/a
27	RAD21	chr14:24900698-24901447	HepG2	liver:	n/a	n/a
28	POLR2A	chr14:24900597-24902065	K562	blood:	n/a	n/a
29	MAZ	chr14:24900878-24901290	GM12878	blood:	n/a	n/a
30	CTCF	chr14:24900907-24901295	A549	lung:	n/a	n/a
31	ZNF384	chr14:24901021-24901264	K562	blood:	n/a	n/a
32	CTCF	chr14:24900936-24901493	Gliobla	brain:	n/a	n/a
33	CTCF	chr14:24901100-24901250	NHDF-neo	bronchial:	n/a	n/a
34	CTCF	chr14:24900858-24901296	K562	blood:	n/a	n/a
35	MXI1	chr14:24900733-24901312	HepG2	liver:	n/a	n/a
36	CHD2	chr14:24901020-24901323	HepG2	liver:	n/a	n/a
37	GTF2F1	chr14:24901140-24901300	K562	blood:	n/a	n/a
38	POLR2A	chr14:24900705-24902088	GM12878	blood:	n/a	n/a
39	RUNX3	chr14:24900948-24901340	GM12878	blood:	n/a	n/a
40	POLR2A	chr14:24900752-24902411	K562	blood:	n/a	n/a
41	POLR2A	chr14:24900908-24902434	A549	lung:	n/a	n/a
42	MAZ	chr14:24900840-24901308	K562	blood:	n/a	n/a
43	CTCF	chr14:24900857-24901331	K562	blood:	n/a	n/a
44	RELA	chr14:24898678-24901293	GM10847	blood:	n/a	chr14:24900296-24900305 chr14:24900296-24900305
45	ELF1	chr14:24898344-24902623	MCF-7	breast:	n/a	chr14:24899135-24899148 chr14:24899076-24899085
46	ZKSCAN1	chr14:24901004-24901317	Hela-S3	cervix:	n/a	n/a
47	RELA	chr14:24898892-24901321	GM18951	blood:	n/a	chr14:24900296-24900305 chr14:24900296-24900305
48	RAD21	chr14:24900783-24901502	SK-N-SH	brain:	n/a	n/a
49	RAD21	chr14:24900819-24901544	MCF-7	breast:	n/a	n/a
50	CTCF	chr14:24900979-24901298	K562	blood:	n/a	n/a

No data

(count:34 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24681602..24685045-chr14:24898549..24902277,4	MCF-7	breast:
2	chr14:24833553..24839988-chr14:24894553..24902357,9	K562	blood:
3	chr14:24833707..24839988-chr14:24896546..24902736,10	K562	blood:
4	chr14:24816528..24849574-chr14:24893305..24914155,145	MCF-7	breast:
5	chr14:24789439..24822082-chr14:24898039..24913135,99	MCF-7	breast:
6	chr14:24813032..24813536-chr14:24900890..24901614,2	MCF-7	breast:
7	chr14:24796890..24797637-chr14:24900960..24901588,2	MCF-7	breast:
8	chr14:24857849..24868599-chr14:24892485..24903992,27	MCF-7	breast:
9	chr14:24711920..24712728-chr14:24900926..24901484,2	K562	blood:
10	chr14:24834576..24835166-chr14:24900643..24901491,2	MCF-7	breast:
11	chr14:24791358..24808812-chr14:24895309..24913599,55	K562	blood:
12	chr14:24778683..24780646-chr14:24900996..24904566,3	K562	blood:
13	chr14:24700875..24703033-chr14:24898892..24902478,3	MCF-7	breast:
14	chr14:24801741..24803463-chr14:24900649..24901597,10	K562	blood:
15	chr14:24802190..24803493-chr14:24900529..24901929,9	MCF-7	breast:
16	chr14:24820479..24821291-chr14:24900677..24901564,2	MCF-7	breast:
17	chr14:24582627..24585556-chr14:24899491..24902320,3	K562	blood:
18	chr14:24709552..24713134-chr14:24898718..24901467,5	MCF-7	breast:
19	chr14:24769087..24772179-chr14:24900488..24904117,5	K562	blood:
20	chr14:24773182..24775572-chr14:24899600..24904217,4	MCF-7	breast:
21	chr14:24881020..24881935-chr14:24900692..24901594,2	K562	blood:
22	chr14:24827418..24850855-chr14:24894884..24913772,127	MCF-7	breast:
23	chr14:24781460..24810019-chr14:24892340..24914262,110	MCF-7	breast:
24	chr14:24834239..24835761-chr14:24900242..24902851,45	MCF-7	breast:
25	chr14:24766804..24771569-chr14:24898237..24903800,5	MCF-7	breast:
26	chr14:24834250..24835522-chr14:24900407..24901666,16	MCF-7	breast:
27	chr14:24768199..24769128-chr14:24900715..24901285,2	K562	blood:
28	chr14:24801057..24801631-chr14:24900679..24901607,3	MCF-7	breast:
29	chr14:24766227..24766812-chr14:24901057..24901559,2	MCF-7	breast:
30	chr14:24800528..24803981-chr14:24898784..24901810,5	K562	blood:
31	chr14:24765284..24770509-chr14:24899183..24903551,4	MCF-7	breast:
32	chr14:24734952..24736987-chr14:24899499..24901815,2	MCF-7	breast:
33	chr14:24796459..24799989-chr14:24897944..24901736,5	K562	blood:
34	chr14:24616178..24618107-chr14:24899295..24902257,2	MCF-7	breast:

No data

Variant related genes	Relation type
KHNYN	TF binding region
CBLN3	TF binding region
ENSG00000129535	Chromatin interaction
ENSG00000100968	Chromatin interaction
ENSG00000255526	Chromatin interaction
ENSG00000205978	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000129559	Chromatin interaction
ENSG00000092098	Chromatin interaction
ENSG00000100897	Chromatin interaction
ENSG00000100911	Chromatin interaction
ENSG00000254692	Chromatin interaction
ENSG00000100949	Chromatin interaction
ENSG00000213903	Chromatin interaction
ENSG00000213920	Chromatin interaction
ENSG00000207141	Chromatin interaction
ENSG00000092330	Chromatin interaction
ENSG00000157379	Chromatin interaction
ENSG00000254505	Chromatin interaction
ENSG00000129465	Chromatin interaction
ENSG00000258973	Chromatin interaction
ENSG00000100938	Chromatin interaction
ENSG00000136305	Chromatin interaction
ENSG00000213906	Chromatin interaction
ENSG00000196943	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs1800876	0.81[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3742520	MMP14	cis	parietal	SCAN
rs3742520	CBLN3	Cis_1M	lymphoblastoid	RTeQTL
rs3742520	KHNYN	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24899600-24901600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
2	chr14:24899800-24901400	Flanking Active TSS	HMEC	breast
3	chr14:24899800-24901600	Flanking Active TSS	HUVEC	blood vessel
4	chr14:24900000-24901400	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr14:24900000-24901600	Enhancers	Fetal Brain Male	brain
6	chr14:24900000-24901600	Enhancers	Fetal Heart	heart
7	chr14:24900000-24901800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
8	chr14:24900000-24902400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr14:24900200-24901400	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
10	chr14:24900200-24901400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
11	chr14:24900200-24901400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
12	chr14:24900200-24901400	Flanking Active TSS	Osteobl	bone
13	chr14:24900200-24906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:24900200-24911000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr14:24900400-24901400	Enhancers	H1 Cell Line	embryonic stem cell
16	chr14:24900400-24901400	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr14:24900400-24901400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr14:24900400-24901400	Weak transcription	Aorta	Aorta
19	chr14:24900400-24901400	Enhancers	Brain Germinal Matrix	brain
20	chr14:24900400-24901400	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
21	chr14:24900400-24901400	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
22	chr14:24900400-24901400	Weak transcription	Psoas Muscle	Psoas
23	chr14:24900400-24901400	Enhancers	K562	blood
24	chr14:24900400-24901600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr14:24900400-24901600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr14:24900400-24901600	Genic enhancers	Primary monocytes fromperipheralblood	blood
27	chr14:24900400-24901600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr14:24900400-24901600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr14:24900400-24901800	Genic enhancers	Left Ventricle	heart
30	chr14:24900400-24901800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
31	chr14:24900400-24902000	Genic enhancers	Spleen	Spleen
32	chr14:24900400-24902400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr14:24900600-24901400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr14:24900600-24901400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr14:24900600-24901400	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
36	chr14:24900600-24901400	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
37	chr14:24900600-24901400	Transcr. at gene 5' and 3'	Right Ventricle	heart
38	chr14:24900600-24901600	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr14:24900600-24901600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr14:24900600-24901600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr14:24900600-24901600	Genic enhancers	Brain Anterior Caudate	brain
42	chr14:24900600-24901600	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
43	chr14:24900600-24901600	Transcr. at gene 5' and 3'	HepG2	liver
44	chr14:24900600-24901600	Transcr. at gene 5' and 3'	HSMM	muscle
45	chr14:24900600-24901600	Transcr. at gene 5' and 3'	NHEK	skin
46	chr14:24900600-24901800	Genic enhancers	Fetal Thymus	thymus
47	chr14:24900600-24902000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr14:24900600-24902000	Genic enhancers	Gastric	stomach
49	chr14:24900600-24902200	Genic enhancers	Placenta	Placenta
50	chr14:24900600-24902200	Genic enhancers	Pancreas	Pancrea

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