Variant report

Variant	rs4301111
Chromosome Location	chr4:15679852-15679853
allele	A/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	STAT3	chr4:15678790-15679953	MCF10A-Er-Src	breast:	n/a	chr4:15679695-15679706 chr4:15679836-15679844
2	EP300	chr4:15679139-15680273	K562	blood:	n/a	n/a
3	FOS	chr4:15678772-15680526	MCF10A-Er-Src	breast:	n/a	chr4:15679403-15679414
4	ARID3A	chr4:15679102-15680659	K562	blood:	n/a	chr4:15680344-15680360 chr4:15680345-15680361
5	NFIC	chr4:15679103-15679915	ECC-1	luminal epithelium:	n/a	n/a
6	FOS	chr4:15678886-15679956	MCF10A-Er-Src	breast:	n/a	chr4:15679403-15679414
7	MYC	chr4:15679181-15679866	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr4:15679439-15679918	K562	blood:	n/a	n/a
9	SRF	chr4:15678960-15679936	HCT-116	colon:	n/a	chr4:15679450-15679468
10	POLR2A	chr4:15678926-15680250	MCF10A-Er-Src	breast:	n/a	n/a
11	IRF1	chr4:15679797-15680275	K562	blood:	n/a	chr4:15680002-15680022
12	SRF	chr4:15678923-15679955	HCT-116	colon:	n/a	chr4:15679450-15679468
13	EBF1	chr4:15679455-15680215	GM12878	blood:	n/a	n/a
14	SRF	chr4:15679021-15679916	MCF-7	breast:	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: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10005305	0.94[AFR][1000 genomes]
rs10008878	0.96[AFR][1000 genomes]
rs10009089	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10017222	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs10025875	0.96[AFR][1000 genomes]
rs10034315	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10516289	1.00[CHB][hapmap]
rs11722757	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11722854	0.81[ASN][1000 genomes]
rs11723478	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11723554	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs11726647	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11729955	1.00[CHB][hapmap]
rs11732953	0.92[AFR][1000 genomes]
rs11735063	0.86[CHB][hapmap]
rs12642407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650529	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13106528	0.88[JPT][hapmap]
rs13131119	0.86[JPT][hapmap]
rs13134177	0.91[AFR][1000 genomes]
rs13141724	0.85[JPT][hapmap]
rs13144428	0.86[JPT][hapmap]
rs13150957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1468735	0.86[JPT][hapmap]
rs1468736	0.82[JPT][hapmap]
rs16892135	0.86[JPT][hapmap]
rs16892143	0.86[JPT][hapmap]
rs16892156	0.82[JPT][hapmap]
rs17405811	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs17476642	1.00[CHB][hapmap]
rs17476670	0.86[JPT][hapmap]
rs1786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041672	0.86[JPT][hapmap]
rs2041673	0.86[JPT][hapmap]
rs28394730	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28402170	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28447067	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28604503	0.81[ASN][1000 genomes]
rs28644177	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28820655	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34473224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34559117	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34831330	0.86[JPT][hapmap]
rs34955342	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35013326	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35120298	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3756247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775956	0.97[AFR][1000 genomes]
rs3775957	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41417147	0.86[JPT][hapmap]
rs4257653	0.98[ASN][1000 genomes]
rs4267734	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs4326008	0.86[JPT][hapmap]
rs4331772	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4346644	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4396986	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4423870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4484296	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549375	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4554069	0.97[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4600905	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698116	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6414764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6449150	0.86[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs6815254	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815296	1.00[CHB][hapmap]
rs6816982	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823775	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6824422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6825051	0.88[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs6825815	0.86[JPT][hapmap]
rs6826058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6827406	1.00[CHB][hapmap];0.82[YRI][hapmap]
rs6828776	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6835038	0.88[JPT][hapmap]
rs6839654	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843740	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844141	0.88[JPT][hapmap]
rs6848779	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs6852735	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6857442	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7434484	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7667175	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698596	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9994518	0.85[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[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
rs4301111	LOC285550	cis	uninvolved skin	skin_eQTL
rs4301111	LOC285550	cis	lesional skin	skin_eQTL
rs4301111	LOC285550	cis	normal skin	skin_eQTL

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	chr4:15671000-15681600	Weak transcription	Fetal Lung	lung
9	chr4:15673200-15680800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr4:15673800-15682800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:15674400-15680400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:15675200-15682600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:15677400-15682800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr4:15677600-15682800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:15677800-15680000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:15677800-15681000	Weak transcription	Primary B cells from cord blood	blood
17	chr4:15678600-15680000	Enhancers	Liver	Liver
18	chr4:15678600-15680200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:15678600-15680200	Enhancers	Fetal Intestine Large	intestine
20	chr4:15678600-15680800	Enhancers	NHLF	lung
21	chr4:15678600-15681200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:15678600-15681600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:15678800-15680000	Enhancers	Duodenum Mucosa	Duodenum
24	chr4:15678800-15680400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:15678800-15681400	Enhancers	Osteobl	bone
26	chr4:15679000-15680000	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr4:15679000-15680000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr4:15679000-15680000	Enhancers	HUVEC	blood vessel
29	chr4:15679000-15680200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:15679000-15680600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:15679000-15680600	Flanking Active TSS	NHEK	skin
32	chr4:15679000-15681200	Enhancers	HepG2	liver
33	chr4:15679000-15681600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:15679000-15681800	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr4:15679000-15682400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr4:15679200-15680200	Enhancers	Fetal Heart	heart
37	chr4:15679200-15681600	Weak transcription	HSMM	muscle
38	chr4:15679200-15682200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:15679400-15680000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
40	chr4:15679400-15680000	Enhancers	Primary hematopoietic stem cells	blood
41	chr4:15679400-15680200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:15679400-15680200	Enhancers	Fetal Intestine Small	intestine
43	chr4:15679400-15681600	Weak transcription	Stomach Mucosa	stomach
44	chr4:15679400-15681800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:15679400-15682200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr4:15679400-15682800	Weak transcription	Pancreas	Pancrea
47	chr4:15679400-15685400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:15679400-15685600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr4:15679600-15680000	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr4:15679600-15680000	Genic enhancers	iPS-20b Cell Line	embryonic stem cell

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