Variant report

Variant	rs4698408
Chromosome Location	chr4:15659048-15659049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:15651703..15660794-chr4:15677607..15686235,25	K562	blood:
2	chr4:15654775..15659231-chr4:15659761..15666940,9	K562	blood:
3	chr4:15649873..15653235-chr4:15657425..15660766,3	MCF-7	breast:
4	chr4:15469326..15470996-chr4:15657243..15660173,2	MCF-7	breast:
5	chr4:15650206..15660298-chr4:15677140..15687517,25	K562	blood:

Variant related genes	Relation type
ENSG00000237765	Chromatin interaction
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10003739	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10008875	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10008889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10012838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10017295	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10020408	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10022610	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10025837	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10026851	0.97[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10030313	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10031017	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10034328	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10939621	1.00[CHB][hapmap]
rs10939628	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1134634	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11932730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11933521	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11939541	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11942335	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11943107	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11945626	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12503015	0.90[EUR][1000 genomes]
rs12508186	0.94[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs12509029	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12511894	0.86[EUR][1000 genomes]
rs12640192	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12644327	0.97[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12649803	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs13116304	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13121363	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1473166	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16892140	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16892141	0.95[JPT][hapmap]
rs16892152	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2041671	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2160044	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28419165	0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs28522268	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28528670	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28534607	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28661857	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3822298	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4235380	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4279203	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs4280723	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4280724	0.86[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4393989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4583752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4591601	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4642244	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4698117	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4698403	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4698405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56041141	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57526178	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs60040560	0.82[EUR][1000 genomes]
rs60813847	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62290605	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6449146	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs6449147	1.00[CHB][hapmap]
rs6449149	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6831286	0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6839438	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73125606	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73125616	0.84[EUR][1000 genomes]
rs73125627	0.86[EUR][1000 genomes]
rs73125637	0.86[EUR][1000 genomes]
rs73127647	0.97[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7377825	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs741180	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs759212	1.00[CHB][hapmap]
rs7661102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7665390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7665915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7682586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7687010	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697314	0.91[CHB][hapmap];0.91[CHD][hapmap]
rs872678	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9996452	0.95[CHB][hapmap];0.91[CHD][hapmap]

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	nsv518830	chr4:15610771-15672200	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4698408	FBXL5	cis	multi-tissue	Pritchard
rs4698408	BOD1L	cis	parietal	SCAN
rs4698408	BST1	cis	multi-tissue	Pritchard
rs4698408	CC2D2A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15657200-15662200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr4:15657600-15681400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:15657800-15659400	Weak transcription	Hela-S3	cervix
4	chr4:15657800-15659400	Weak transcription	HepG2	liver
5	chr4:15657800-15659600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:15657800-15659800	Weak transcription	A549	lung
7	chr4:15657800-15660000	Enhancers	NHDF-Ad	bronchial
8	chr4:15657800-15661400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:15657800-15666800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:15657800-15667800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:15658000-15659200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:15658000-15659200	Weak transcription	K562	blood
13	chr4:15658000-15659800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:15658000-15660600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr4:15658000-15661400	Weak transcription	Placenta	Placenta
16	chr4:15658000-15664600	Weak transcription	Esophagus	oesophagus
17	chr4:15658000-15665400	Weak transcription	Psoas Muscle	Psoas
18	chr4:15658000-15666800	Weak transcription	Thymus	Thymus
19	chr4:15658000-15667400	Weak transcription	Fetal Muscle Leg	muscle
20	chr4:15658000-15667800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:15658000-15672200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:15658000-15673800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:15658000-15675200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:15658000-15679000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:15658000-15681400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:15658200-15659200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:15658200-15659400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:15658200-15659400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:15658200-15659400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr4:15658200-15659600	Enhancers	Osteobl	bone
31	chr4:15658200-15659800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:15658200-15660200	Enhancers	Fetal Lung	lung
33	chr4:15658200-15660400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:15658200-15661000	Weak transcription	Fetal Heart	heart
35	chr4:15658200-15661200	Weak transcription	Liver	Liver
36	chr4:15658200-15661600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:15658200-15661800	Active TSS	Primary B cells from cord blood	blood
38	chr4:15658200-15665000	Weak transcription	GM12878-XiMat	blood
39	chr4:15658200-15666600	Weak transcription	HUVEC	blood vessel
40	chr4:15658200-15666800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:15658200-15667200	Weak transcription	Fetal Thymus	thymus
42	chr4:15658200-15667400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr4:15658200-15667400	Weak transcription	NH-A	brain
44	chr4:15658200-15667800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr4:15658200-15667800	Weak transcription	NHLF	lung
46	chr4:15658200-15668000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:15658200-15670600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr4:15658200-15679200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:15658200-15679200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr4:15658200-15682200	Weak transcription	Fetal Stomach	stomach

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