Variant report

Variant	rs4072391
Chromosome Location	chr1:154438880-154438881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154317108..154317820-chr1:154438724..154439547,2	MCF-7	breast:
2	chr1:154427927..154430760-chr1:154437313..154439105,2	K562	blood:
3	chr1:154377223..154380396-chr1:154438444..154440442,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228013	Chromatin interaction
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10047079	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10752641	0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10908839	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11490956	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12403537	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12405637	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12406822	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12408461	0.84[CEU][hapmap];0.89[CHB][hapmap];0.88[EUR][1000 genomes]
rs2229238	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35699331	0.91[ASN][1000 genomes]
rs3811448	0.84[CEU][hapmap];0.89[CHB][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs3811449	0.88[EUR][1000 genomes]
rs41269915	0.87[EUR][1000 genomes]
rs41308419	0.87[EUR][1000 genomes]
rs41313910	0.88[EUR][1000 genomes]
rs4240872	0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs4240873	0.82[YRI][hapmap]
rs4341355	0.80[CEU][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4379670	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4390168	0.84[CEU][hapmap];0.89[CHB][hapmap];0.86[EUR][1000 genomes]
rs4393148	0.88[YRI][hapmap]
rs4509570	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4633282	0.87[EUR][1000 genomes]
rs4639752	0.84[CEU][hapmap];0.89[CHB][hapmap];0.87[EUR][1000 genomes]
rs4845632	0.88[YRI][hapmap]
rs4845646	0.84[YRI][hapmap]
rs55668699	0.83[ASN][1000 genomes]
rs57783436	0.88[EUR][1000 genomes]
rs58348886	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58710275	0.87[EUR][1000 genomes]
rs58881140	0.88[EUR][1000 genomes]
rs59084843	0.88[EUR][1000 genomes]
rs59239860	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59741504	0.87[EUR][1000 genomes]
rs59838898	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60092776	0.88[EUR][1000 genomes]
rs60255122	0.86[EUR][1000 genomes]
rs60368585	0.87[EUR][1000 genomes]
rs60498985	0.88[EUR][1000 genomes]
rs60760897	0.86[EUR][1000 genomes]
rs60931472	0.88[EUR][1000 genomes]
rs61275241	0.86[EUR][1000 genomes]
rs61403567	0.86[EUR][1000 genomes]
rs61559765	0.88[EUR][1000 genomes]
rs61698846	0.86[EUR][1000 genomes]
rs6427672	0.86[ASN][1000 genomes]
rs6669229	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6672087	0.84[CEU][hapmap];0.89[CHB][hapmap];0.88[EUR][1000 genomes]
rs6674171	0.90[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6678164	0.84[YRI][hapmap]
rs6681207	0.84[CEU][hapmap];0.89[CHB][hapmap];0.88[EUR][1000 genomes]
rs6683078	0.88[YRI][hapmap]
rs6684225	0.84[YRI][hapmap]
rs6687597	0.91[ASN][1000 genomes]
rs6698040	0.91[ASN][1000 genomes]
rs72999415	0.88[EUR][1000 genomes]
rs72999419	0.88[EUR][1000 genomes]
rs72999422	0.88[EUR][1000 genomes]
rs73018293	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73020232	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73020234	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73020246	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73023331	0.87[EUR][1000 genomes]
rs73023339	0.87[EUR][1000 genomes]
rs73023346	0.88[EUR][1000 genomes]
rs73023348	0.88[EUR][1000 genomes]
rs73023349	0.88[EUR][1000 genomes]
rs7514452	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7526293	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7530737	0.81[YRI][hapmap]
rs7537291	0.91[ASN][1000 genomes]
rs7537316	0.91[ASN][1000 genomes]
rs7539745	0.80[YRI][hapmap]
rs7546068	0.91[ASN][1000 genomes]
rs7546552	0.91[ASN][1000 genomes]
rs7546555	0.91[ASN][1000 genomes]
rs7551873	0.84[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs7556449	0.84[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4072391	LCE3C	cis	cerebellum	SCAN
rs4072391	ARNT	cis	cerebellum	SCAN
rs4072391	PI4KB	cis	parietal	SCAN
rs4072391	ADAMTSL4	cis	parietal	SCAN
rs4072391	TDRD10	cis	lung	GTEx
rs4072391	PMF1	cis	cerebellum	SCAN
rs4072391	PMF1	cis	parietal	SCAN
rs4072391	CDC42SE1	cis	parietal	SCAN
rs4072391	LCE3A	cis	parietal	SCAN
rs4072391	CDC42SE1	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154418000-154440000	Weak transcription	Small Intestine	intestine
2	chr1:154426600-154440600	Weak transcription	Brain Angular Gyrus	brain
3	chr1:154426800-154441200	Weak transcription	Brain Substantia Nigra	brain
4	chr1:154426800-154442200	Weak transcription	HepG2	liver
5	chr1:154426800-154450000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:154427800-154464800	Weak transcription	Ovary	ovary
7	chr1:154429800-154446200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:154431600-154441400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:154432000-154442000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:154434800-154439600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:154435200-154441000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:154435600-154440000	Enhancers	Primary hematopoietic stem cells	blood
13	chr1:154435600-154441400	Enhancers	Fetal Thymus	thymus
14	chr1:154436000-154439000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:154436200-154440800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:154436200-154441000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:154436200-154441200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:154436400-154441800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:154436400-154446400	Weak transcription	NHEK	skin
20	chr1:154436400-154446600	Weak transcription	HMEC	breast
21	chr1:154436600-154439400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:154436600-154440600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:154436600-154441000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:154436600-154441200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr1:154436600-154441200	Weak transcription	Fetal Brain Male	brain
26	chr1:154436600-154441600	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr1:154436600-154441600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:154436600-154446800	Weak transcription	NHDF-Ad	bronchial
29	chr1:154436600-154450600	Weak transcription	HUVEC	blood vessel
30	chr1:154437200-154439200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:154437200-154439400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr1:154437200-154441600	Strong transcription	Lung	lung
33	chr1:154437400-154439000	Strong transcription	Left Ventricle	heart
34	chr1:154437400-154442000	Weak transcription	Colonic Mucosa	Colon
35	chr1:154437600-154439000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:154437600-154439000	Strong transcription	Colon Smooth Muscle	Colon
37	chr1:154437600-154439200	Enhancers	Thymus	Thymus
38	chr1:154437600-154439600	Genic enhancers	Primary monocytes fromperipheralblood	blood
39	chr1:154437800-154439400	Genic enhancers	Stomach Smooth Muscle	stomach
40	chr1:154437800-154440200	Genic enhancers	Monocytes-CD14+_RO01746	blood
41	chr1:154437800-154440400	Enhancers	GM12878-XiMat	blood
42	chr1:154437800-154442800	Enhancers	Brain Hippocampus Middle	brain
43	chr1:154438000-154439400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:154438000-154439600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:154438000-154442600	Weak transcription	Fetal Stomach	stomach
46	chr1:154438200-154439000	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr1:154438200-154439200	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr1:154438200-154441400	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr1:154438200-154442200	Weak transcription	Stomach Mucosa	stomach
50	chr1:154438400-154439000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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