Variant report

Variant	rs7434484
Chromosome Location	chr4:15679371-15679372
allele	C/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	CEBPB	chr4:15679248-15679726	Hela-S3	cervix:	n/a	n/a
2	SRF	chr4:15679053-15679744	ECC-1	luminal epithelium:	n/a	chr4:15679450-15679468
3	POLR2A	chr4:15679345-15679513	HepG2	liver:	n/a	n/a
4	STAT3	chr4:15678790-15679953	MCF10A-Er-Src	breast:	n/a	chr4:15679695-15679706 chr4:15679836-15679844
5	EP300	chr4:15679139-15680273	K562	blood:	n/a	n/a
6	YY1	chr4:15679347-15679666	HCT-116	colon:	n/a	n/a
7	TBP	chr4:15679252-15679598	Hela-S3	cervix:	n/a	n/a
8	NFIC	chr4:15679240-15679609	HepG2	liver:	n/a	n/a
9	NFIC	chr4:15679101-15679844	ECC-1	luminal epithelium:	n/a	n/a
10	MAZ	chr4:15679117-15679535	K562	blood:	n/a	n/a
11	CTCF	chr4:15679340-15679490	SAEC	small airway:	n/a	n/a
12	JUND	chr4:15678865-15679551	HepG2	liver:	n/a	chr4:15679202-15679213
13	FOS	chr4:15678772-15680526	MCF10A-Er-Src	breast:	n/a	chr4:15679403-15679414
14	TBP	chr4:15679362-15679493	K562	blood:	n/a	n/a
15	SRF	chr4:15679130-15679772	MCF-7	breast:	n/a	chr4:15679450-15679468
16	POLR2A	chr4:15679265-15679568	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr4:15679172-15679675	Hela-S3	cervix:	n/a	n/a
18	FOS	chr4:15678814-15679674	MCF10A-Er-Src	breast:	n/a	chr4:15679403-15679414
19	FOS	chr4:15678662-15679792	MCF10A-Er-Src	breast:	n/a	chr4:15679403-15679414
20	POLR2A	chr4:15679200-15679536	Hela-S3	cervix:	n/a	n/a
21	SRF	chr4:15678992-15679823	ECC-1	luminal epithelium:	n/a	chr4:15679450-15679468
22	STAT3	chr4:15679224-15679591	Hela-S3	cervix:	n/a	n/a
23	NFIC	chr4:15679240-15679718	SK-N-SH	brain:	n/a	n/a
24	ARID3A	chr4:15679102-15680659	K562	blood:	n/a	chr4:15680344-15680360 chr4:15680345-15680361
25	NFIC	chr4:15679103-15679915	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr4:15679205-15679396	K562	blood:	n/a	n/a
27	USF2	chr4:15679349-15679558	Hela-S3	cervix:	n/a	n/a
28	RCOR1	chr4:15679332-15679480	HepG2	liver:	n/a	n/a
29	JUND	chr4:15678534-15679672	K562	blood:	n/a	chr4:15679202-15679213
30	YY1	chr4:15679311-15679647	ECC-1	luminal epithelium:	n/a	n/a
31	ATF1	chr4:15679256-15679597	K562	blood:	n/a	n/a
32	STAT3	chr4:15679355-15679664	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr4:15678622-15679823	MCF10A-Er-Src	breast:	n/a	n/a
34	SRF	chr4:15679292-15679596	K562	blood:	n/a	chr4:15679450-15679468
35	FOSL2	chr4:15678913-15679692	SK-N-SH	brain:	n/a	chr4:15679404-15679415
36	JUND	chr4:15678896-15679626	Hela-S3	cervix:	n/a	chr4:15679202-15679213
37	FOS	chr4:15678886-15679956	MCF10A-Er-Src	breast:	n/a	chr4:15679403-15679414
38	TEAD4	chr4:15679281-15679722	ECC-1	luminal epithelium:	n/a	n/a
39	ELK4	chr4:15679258-15679665	Hela-S3	cervix:	n/a	n/a
40	BHLHE40	chr4:15679136-15679611	K562	blood:	n/a	n/a
41	SRF	chr4:15679285-15679666	K562	blood:	n/a	chr4:15679450-15679468
42	MYC	chr4:15679181-15679866	MCF10A-Er-Src	breast:	n/a	n/a
43	ELK1	chr4:15679283-15679511	K562	blood:	n/a	n/a
44	FOS	chr4:15678578-15679694	HUVEC	blood vessel:	n/a	chr4:15679403-15679414
45	SP1	chr4:15679057-15679615	A549	lung:	n/a	n/a
46	POLR2A	chr4:15679206-15679627	Hela-S3	cervix:	n/a	n/a
47	TCF12	chr4:15679088-15679650	ECC-1	luminal epithelium:	n/a	n/a
48	RCOR1	chr4:15679118-15679691	Hela-S3	cervix:	n/a	n/a
49	MYC	chr4:15679235-15679682	K562	blood:	n/a	n/a
50	SRF	chr4:15678960-15679936	HCT-116	colon:	n/a	chr4:15679450-15679468

No.	Distal block	Cell Line	Cell type
1	chr4:15662285..15665284-chr4:15678264..15680948,2	MCF-7	breast:
2	chr4:15673240..15674969-chr4:15677739..15681015,3	MCF-7	breast:
3	chr4:15651703..15660794-chr4:15677607..15686235,25	K562	blood:
4	chr4:15652080..15658606-chr4:15677363..15685579,17	MCF-7	breast:
5	chr4:15650206..15660298-chr4:15677140..15687517,25	K562	blood:

Variant related genes	Relation type
FAM200B	TF binding region
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10005305	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10008878	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10015827	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10017222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10025875	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10433813	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10516289	1.00[CHB][hapmap]
rs11722300	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11722854	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723554	1.00[CHB][hapmap]
rs11729955	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11730088	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11732953	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11735063	1.00[CHB][hapmap]
rs11947383	0.80[CEU][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs12642407	0.81[ASN][1000 genomes]
rs13134177	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17405811	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17476642	1.00[CHB][hapmap]
rs1786	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs28394730	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28402170	0.81[ASN][1000 genomes]
rs28604503	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28644177	0.81[ASN][1000 genomes]
rs28820655	0.81[ASN][1000 genomes]
rs34473224	0.81[ASN][1000 genomes]
rs34559117	0.81[ASN][1000 genomes]
rs3756247	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs3775956	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4301111	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs4396986	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs4423870	1.00[CHB][hapmap]
rs4484296	0.81[ASN][1000 genomes]
rs4549375	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs4554069	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414764	1.00[CHB][hapmap]
rs6449152	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6815254	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6815296	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6816982	0.81[ASN][1000 genomes]
rs6824422	1.00[CHB][hapmap]
rs6826058	1.00[CHB][hapmap]
rs6827406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6839654	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6843740	0.81[ASN][1000 genomes]
rs6848779	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7667175	0.81[ASN][1000 genomes]
rs7698596	0.81[ASN][1000 genomes]
rs9994518	0.88[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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 target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv3361772	chr4:15666732-15684418	Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7434484	FAM200B	cis	cerebellum	SCAN
rs7434484	FBXL5	Cis_1M	lymphoblastoid	RTeQTL
rs7434484	FAM200B	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15657600-15681400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:15658000-15681400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:15658200-15682200	Weak transcription	Fetal Stomach	stomach
4	chr4:15664800-15681800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:15668400-15682800	Weak transcription	Fetal Brain Male	brain
6	chr4:15668600-15681400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:15669600-15681400	Weak transcription	Thymus	Thymus
8	chr4:15671000-15679400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:15671000-15681600	Weak transcription	Fetal Lung	lung
10	chr4:15673200-15680800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr4:15673800-15682800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:15674400-15680400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:15675200-15682600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:15677400-15682800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:15677600-15682800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:15677800-15680000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:15677800-15681000	Weak transcription	Primary B cells from cord blood	blood
18	chr4:15678600-15679600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:15678600-15679600	Flanking Active TSS	A549	lung
20	chr4:15678600-15679800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:15678600-15679800	Enhancers	HMEC	breast
22	chr4:15678600-15680000	Enhancers	Liver	Liver
23	chr4:15678600-15680200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:15678600-15680200	Enhancers	Fetal Intestine Large	intestine
25	chr4:15678600-15680800	Enhancers	NHLF	lung
26	chr4:15678600-15681200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:15678600-15681600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:15678800-15679600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:15678800-15679800	Flanking Active TSS	K562	blood
30	chr4:15678800-15680000	Enhancers	Duodenum Mucosa	Duodenum
31	chr4:15678800-15680400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:15678800-15681400	Enhancers	Osteobl	bone
33	chr4:15679000-15679400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:15679000-15679400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:15679000-15679400	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr4:15679000-15679400	Enhancers	Pancreas	Pancrea
37	chr4:15679000-15679400	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr4:15679000-15679400	Enhancers	Stomach Mucosa	stomach
39	chr4:15679000-15679600	Enhancers	H1 Cell Line	embryonic stem cell
40	chr4:15679000-15679600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:15679000-15679600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr4:15679000-15679600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:15679000-15679600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:15679000-15679600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr4:15679000-15679600	Transcr. at gene 5' and 3'	Dnd41	blood
46	chr4:15679000-15679800	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr4:15679000-15679800	Flanking Active TSS	Hela-S3	cervix
48	chr4:15679000-15680000	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr4:15679000-15680000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr4:15679000-15680000	Enhancers	HUVEC	blood vessel

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