Variant report

Variant	rs2296482
Chromosome Location	chr14:104029819-104029820
allele	A/C
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	ELF1	chr14:104028738-104029826	MCF-7	breast:	n/a	chr14:104029076-104029088 chr14:104029239-104029248 chr14:104029097-104029106
2	TAF1	chr14:104028177-104029827	ECC-1	luminal epithelium:	n/a	n/a
3	SIN3AK20	chr14:104028608-104029969	MCF-7	breast:	n/a	n/a
4	RFX5	chr14:104028739-104029954	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr14:104027997-104029923	HUVEC	blood vessel:	n/a	n/a
6	MAX	chr14:104027988-104029903	ECC-1	luminal epithelium:	n/a	n/a
7	MAZ	chr14:104028756-104029978	HepG2	liver:	n/a	n/a
8	POLR2A	chr14:104028089-104029853	K562	blood:	n/a	n/a
9	TFAP2A	chr14:104028374-104029968	Hela-S3	cervix:	n/a	chr14:104029549-104029564 chr14:104029518-104029533
10	EGR1	chr14:104028226-104029823	MCF-7	breast:	n/a	n/a
11	MYC	chr14:104028935-104029882	MCF10A-Er-Src	breast:	n/a	n/a
12	SIN3AK20	chr14:104028703-104029823	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3A	chr14:104027720-104030129	H1-hESC	embryonic stem cell:	n/a	chr14:104028758-104028771 chr14:104028792-104028805 chr14:104028844-104028855 chr14:104028533-104028544 chr14:104028851-104028864 chr14:104029113-104029126 chr14:104029095-104029108
14	MTA3	chr14:104028613-104030052	GM12878	blood:	n/a	n/a
15	ZNF384	chr14:104029700-104030048	GM12878	blood:	n/a	n/a
16	POLR2A	chr14:104028182-104029832	HUVEC	blood vessel:	n/a	n/a
17	HDAC2	chr14:104028201-104029826	MCF-7	breast:	n/a	n/a
18	HCFC1	chr14:104027237-104030166	Hela-S3	cervix:	n/a	n/a
19	SIN3AK20	chr14:104027394-104030066	MCF-7	breast:	n/a	n/a
20	MXI1	chr14:104028044-104030134	IMR90	lung:	n/a	n/a
21	CTCF	chr14:104029680-104029830	SAEC	small airway:	n/a	n/a
22	REST	chr14:104027727-104029942	H1-neurons	neurons:	n/a	chr14:104028758-104028771 chr14:104028121-104028130 chr14:104028792-104028805 chr14:104028123-104028130 chr14:104029104-104029117 chr14:104028789-104028802 chr14:104028796-104028805
23	TFAP2C	chr14:104028326-104029931	Hela-S3	cervix:	n/a	chr14:104029549-104029564
24	POLR2A	chr14:104027824-104030167	GM12891	blood:	n/a	n/a
25	HA-E2F1	chr14:104027559-104029847	MCF-7	breast:	n/a	chr14:104028207-104028221 chr14:104028209-104028217 chr14:104028209-104028217 chr14:104028673-104028688 chr14:104029236-104029245
26	MAX	chr14:104028156-104029838	HepG2	liver:	n/a	n/a
27	MAX	chr14:104028706-104029895	GM12878	blood:	n/a	n/a
28	CHD2	chr14:104028267-104029838	GM12878	blood:	n/a	chr14:104028711-104028721 chr14:104029283-104029293
29	TCF12	chr14:104029028-104029859	ECC-1	luminal epithelium:	n/a	n/a
30	GABPA	chr14:104027612-104029881	MCF-7	breast:	n/a	n/a
31	MXI1	chr14:104027798-104030910	SK-N-SH	brain:	n/a	chr14:104030620-104030635 chr14:104030622-104030637
32	YY1	chr14:104028193-104029826	SK-N-SH	brain:	n/a	chr14:104028385-104028399 chr14:104029236-104029245 chr14:104029027-104029038 chr14:104029239-104029248 chr14:104029234-104029248
33	MAX	chr14:104028116-104029857	A549	lung:	n/a	n/a
34	POLR2A	chr14:104027621-104029923	MCF10A-Er-Src	breast:	n/a	n/a
35	IRF1	chr14:104029803-104029983	K562	blood:	n/a	n/a
36	MXI1	chr14:104028829-104029854	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr14:104027750-104030033	Hela-S3	cervix:	n/a	n/a
38	MAX	chr14:104027574-104029883	MCF-7	breast:	n/a	n/a
39	GABPA	chr14:104028097-104029914	MCF-7	breast:	n/a	n/a
40	ZMIZ1	chr14:104028667-104029883	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:104026845..104031617-chr14:104090112..104098528,12	MCF-7	breast:
2	chr14:104016689..104020988-chr14:104027518..104030448,6	MCF-7	breast:
3	chr14:103992721..103998040-chr14:104027797..104030842,4	MCF-7	breast:
4	chr14:104026026..104030833-chr14:104180410..104184978,6	MCF-7	breast:
5	chr14:104026574..104032100-chr14:104033737..104038565,9	MCF-7	breast:
6	chr14:103985364..103989946-chr14:104026445..104030227,8	MCF-7	breast:
7	chr14:104027061..104029959-chr14:104033088..104037337,3	K562	blood:
8	chr14:104027886..104033252-chr14:104178637..104183670,7	MCF-7	breast:
9	chr14:103995545..103997122-chr14:104028296..104030375,2	K562	blood:
10	chr14:104026767..104030601-chr14:104092111..104097061,5	MCF-7	breast:

Variant related genes	Relation type
BAG5	TF binding region
RNU4-68P	TF binding region
ENSG00000260285	Chromatin interaction
ENSG00000256053	Chromatin interaction
ENSG00000166165	Chromatin interaction
ENSG00000126214	Chromatin interaction
ENSG00000258851	Chromatin interaction
ENSG00000269963	Chromatin interaction
ENSG00000126215	Chromatin interaction
ENSG00000166166	Chromatin interaction
ENSG00000100711	Chromatin interaction
ENSG00000201184	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10431750	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11844466	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11846404	0.85[CHD][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap]
rs11851000	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11851616	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12884809	0.88[CHD][hapmap];0.91[MEX][hapmap]
rs12887734	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12889403	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12889721	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12890820	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12892038	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12894729	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273175	0.87[MEX][hapmap]
rs2274267	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403196	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2403197	0.88[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2896487	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34026011	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34186780	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34843146	0.80[ASN][1000 genomes]
rs34896432	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35026580	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35229468	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35496194	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35498576	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4525427	0.82[ASN][1000 genomes]
rs4900590	0.80[JPT][hapmap]
rs4906335	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4906336	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4906337	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4906338	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4906356	0.85[CHD][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap]
rs55751606	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57072546	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs58033365	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60249782	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs67899457	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7140568	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71417868	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7148456	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs729438	0.80[CHD][hapmap]
rs8017628	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8017993	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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 miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv902297	chr14:103956182-104061646	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902298	chr14:103959289-104061646	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv902299	chr14:103967504-104061646	Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv902303	chr14:103979953-104034746	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv902304	chr14:103979953-104061646	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	nsv902305	chr14:103979953-104073551	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
10	esv1839595	chr14:103987140-104034746	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
11	nsv566022	chr14:104007555-104092789	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	esv3389476	chr14:104028349-104030447	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2296482	ZFYVE21	cis	cerebellum	SCAN
rs2296482	C14orf153	cis	parietal	SCAN
rs2296482	C14orf153	cis	cerebellum	SCAN
rs2296482	MARK3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104027400-104030600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr14:104027400-104030800	Active TSS	H1 Cell Line	embryonic stem cell
3	chr14:104027400-104030800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr14:104027600-104030200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr14:104027600-104030200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr14:104027600-104030200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr14:104027600-104030400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr14:104027600-104030400	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr14:104027600-104030400	Active TSS	Esophagus	oesophagus
10	chr14:104027600-104030600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:104027600-104030800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr14:104027600-104030800	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr14:104027600-104030800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr14:104027600-104030800	Active TSS	NHLF	lung
15	chr14:104027800-104030000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr14:104027800-104030000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr14:104027800-104030000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr14:104027800-104030000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr14:104027800-104030200	Active TSS	Gastric	stomach
20	chr14:104027800-104030200	Active TSS	GM12878-XiMat	blood
21	chr14:104027800-104030200	Active TSS	Hela-S3	cervix
22	chr14:104027800-104030400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr14:104027800-104030400	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr14:104027800-104030400	Active TSS	Fetal Kidney	kidney
25	chr14:104027800-104030400	Active TSS	Ovary	ovary
26	chr14:104027800-104030400	Active TSS	HMEC	breast
27	chr14:104027800-104030600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr14:104027800-104030600	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr14:104027800-104030600	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr14:104027800-104030600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr14:104027800-104030600	Active TSS	A549	lung
32	chr14:104027800-104030600	Active TSS	HSMM	muscle
33	chr14:104027800-104030800	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr14:104028000-104030200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr14:104028000-104030200	Active TSS	Fetal Intestine Large	intestine
36	chr14:104028000-104030200	Active TSS	Fetal Intestine Small	intestine
37	chr14:104028000-104030200	Active TSS	Lung	lung
38	chr14:104028000-104030200	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr14:104028000-104030200	Active TSS	NHEK	skin
40	chr14:104028000-104030400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr14:104028000-104030400	Active TSS	Fetal Lung	lung
42	chr14:104028000-104030600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr14:104028000-104030600	Active TSS	Psoas Muscle	Psoas
44	chr14:104028000-104030600	Active TSS	NHDF-Ad	bronchial
45	chr14:104028200-104030000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr14:104028200-104030000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr14:104028200-104030000	Active TSS	Fetal Stomach	stomach
48	chr14:104028200-104030200	Active TSS	Left Ventricle	heart
49	chr14:104028200-104030200	Active TSS	Rectal Smooth Muscle	rectum
50	chr14:104028200-104030600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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