Variant report

Variant	rs12445041
Chromosome Location	chr16:82194190-82194191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:82192940..82199910-chr16:82200069..82205182,12	MCF-7	breast:
2	chr16:82185992..82189074-chr16:82193243..82196142,4	MCF-7	breast:
3	chr16:82192311..82195081-chr16:82198371..82200683,2	K562	blood:
4	chr16:82185306..82186813-chr16:82193802..82195374,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135698	Chromatin interaction
ENSG00000261029	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1056675	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs1064208	1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12446210	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs12448920	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12598637	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs1424155	0.82[CEU][hapmap];0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs1559425	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs17232243	0.85[YRI][hapmap]
rs17232307	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs1834053	0.87[EUR][1000 genomes]
rs1862820	0.82[CEU][hapmap];0.81[CHB][hapmap];0.89[TSI][hapmap]
rs1862822	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs1987155	0.90[EUR][1000 genomes]
rs2288050	0.85[CEU][hapmap]
rs2303266	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes]
rs2911378	0.81[EUR][1000 genomes]
rs2911379	0.80[EUR][1000 genomes]
rs2911380	0.92[EUR][1000 genomes]
rs2911381	0.80[EUR][1000 genomes]
rs2911382	0.80[EUR][1000 genomes]
rs2911383	0.85[CHB][hapmap]
rs2911385	0.84[CHB][hapmap];0.81[EUR][1000 genomes]
rs2911386	0.81[EUR][1000 genomes]
rs2911388	0.81[EUR][1000 genomes]
rs2911389	0.92[CEU][hapmap];0.81[CHB][hapmap];0.92[EUR][1000 genomes]
rs2911391	0.82[CEU][hapmap];0.81[CHB][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs2911392	0.81[EUR][1000 genomes]
rs2911393	0.92[EUR][1000 genomes]
rs2911394	0.81[EUR][1000 genomes]
rs2911396	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs2967327	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs2967332	0.93[EUR][1000 genomes]
rs2967365	0.92[EUR][1000 genomes]
rs2967366	0.80[EUR][1000 genomes]
rs2967367	0.80[EUR][1000 genomes]
rs2967369	0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs2967370	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs2967371	0.80[CEU][hapmap];0.85[CHB][hapmap];0.80[EUR][1000 genomes]
rs3829545	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[EUR][1000 genomes]
rs3829546	0.80[EUR][1000 genomes]
rs3829547	0.92[EUR][1000 genomes]
rs3829549	0.81[EUR][1000 genomes]
rs3829550	0.93[EUR][1000 genomes]
rs3898333	0.91[EUR][1000 genomes]
rs41534745	0.85[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4888208	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4889467	0.81[EUR][1000 genomes]
rs4889476	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[EUR][1000 genomes]
rs56116174	0.88[EUR][1000 genomes]
rs7196560	0.80[EUR][1000 genomes]
rs7205347	0.97[EUR][1000 genomes]
rs7206501	0.82[EUR][1000 genomes]
rs7405197	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs918759	0.81[CHB][hapmap];0.93[GIH][hapmap]
rs918760	0.81[CHB][hapmap]
rs978971	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532598	chr16:82034475-82738733	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv532599	chr16:82074439-82926863	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv457578	chr16:82136566-82197883	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv573366	chr16:82136566-82197883	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv573367	chr16:82140561-83040846	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv457579	chr16:82150293-82216622	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv573368	chr16:82150293-82216622	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv907013	chr16:82154619-82196808	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv525467	chr16:82154619-82223485	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1061064	chr16:82165314-82213799	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1056381	chr16:82165314-82215388	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1062687	chr16:82165516-82213799	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv518129	chr16:82188173-82228076	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv833302	chr16:82188351-82363863	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12445041	MPHOSPH6	cis	parietal	SCAN
rs12445041	MPHOSPH6	cis	Stomach	GTEx
rs12445041	MPHOSPH6	cis	lymphoblastoid	seeQTL
rs12445041	MPHOSPH6	Cis_1M	lymphoblastoid	RTeQTL
rs12445041	MPHOSPH6	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:82168000-82195400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr16:82168400-82195600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr16:82168600-82195600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr16:82170800-82195800	Weak transcription	Colon Smooth Muscle	Colon
5	chr16:82172800-82199200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr16:82173400-82203000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr16:82177000-82195200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr16:82179200-82196000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr16:82179800-82196200	Weak transcription	Fetal Heart	heart
10	chr16:82180800-82195600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr16:82181200-82194200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr16:82181200-82195800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr16:82181200-82196600	Weak transcription	Small Intestine	intestine
14	chr16:82181600-82194600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr16:82181600-82195400	Weak transcription	GM12878-XiMat	blood
16	chr16:82181800-82194200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr16:82184200-82194400	Weak transcription	NH-A	brain
18	chr16:82186000-82199200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr16:82186000-82201600	Strong transcription	Primary T cells from cord blood	blood
20	chr16:82186400-82202800	Weak transcription	Psoas Muscle	Psoas
21	chr16:82186600-82194200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr16:82186600-82202600	Weak transcription	Stomach Mucosa	stomach
23	chr16:82187400-82200600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr16:82188400-82202200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr16:82189200-82194800	Weak transcription	Fetal Kidney	kidney
26	chr16:82189800-82199200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr16:82190200-82195800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr16:82191000-82201000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr16:82191200-82199200	Strong transcription	Primary B cells from cord blood	blood
30	chr16:82191200-82200800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr16:82191200-82201000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr16:82191400-82201000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr16:82191600-82194400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr16:82191800-82198800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr16:82192000-82200400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr16:82192400-82200800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr16:82192600-82198000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr16:82192600-82198200	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr16:82192600-82201200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr16:82193000-82199200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr16:82193000-82200400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr16:82193000-82201600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr16:82193200-82194400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr16:82193200-82197400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr16:82193200-82197800	Strong transcription	A549	lung
46	chr16:82193200-82198000	Strong transcription	Brain Anterior Caudate	brain
47	chr16:82193200-82198200	Strong transcription	HSMMtube	muscle
48	chr16:82193200-82198400	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr16:82193200-82199800	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr16:82193200-82200000	Strong transcription	Primary B cells from peripheral blood	blood

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