Variant report

Variant	rs9944207
Chromosome Location	chr15:75912889-75912890
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	chr15:75912823-75913528	MCF10A-Er-Src	breast:	n/a	chr15:75912964-75912975
2	STAT3	chr15:75912737-75913471	MCF10A-Er-Src	breast:	n/a	chr15:75912964-75912975
3	CEBPB	chr15:75912884-75913079	K562	blood:	n/a	chr15:75912985-75912997
4	CEBPB	chr15:75912381-75913840	IMR90	lung:	n/a	chr15:75912484-75912501 chr15:75912985-75912997 chr15:75912538-75912549
5	CEBPB	chr15:75912504-75913020	Hela-S3	cervix:	n/a	chr15:75912985-75912997 chr15:75912538-75912549
6	FOS	chr15:75912855-75913787	MCF10A-Er-Src	breast:	n/a	chr15:75913559-75913566 chr15:75913556-75913567 chr15:75913558-75913566 chr15:75913540-75913549 chr15:75913558-75913567
7	MYC	chr15:75912743-75912965	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr15:75912769-75912987	NB4	blood:	n/a	n/a
9	STAT3	chr15:75912787-75913486	MCF10A-Er-Src	breast:	n/a	chr15:75912964-75912975
10	MYC	chr15:75912794-75913675	MCF10A-Er-Src	breast:	n/a	chr15:75913557-75913566

No.	Distal block	Cell Line	Cell type
1	chr15:75911907..75914584-chr15:75917621..75920506,2	MCF-7	breast:
2	chr15:75871075..75873758-chr15:75910393..75912926,2	K562	blood:
3	chr15:75911354..75914266-chr15:75928141..75929815,2	MCF-7	breast:
4	chr15:75911547..75913096-chr15:75931210..75932754,2	MCF-7	breast:
5	chr15:75907827..75910808-chr15:75911030..75912891,2	K562	blood:
6	chr15:75743771..75747825-chr15:75911838..75914766,3	MCF-7	breast:
7	chr15:75912520..75914739-chr15:75915567..75919669,4	K562	blood:

Variant related genes	Relation type
SNUPN	TF binding region
ENSG00000260235	TF binding region
ENSG00000177971	Chromatin interaction
ENSG00000169371	Chromatin interaction
ENSG00000260235	Chromatin interaction
ENSG00000260206	Chromatin interaction
ENSG00000169375	Chromatin interaction
ENSG00000169410	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10163126	0.88[ASN][1000 genomes]
rs11072552	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11072553	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11634402	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11635080	0.82[EUR][1000 genomes]
rs11636031	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11636199	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11638974	1.00[CEU][hapmap]
rs11856606	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs12101874	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12708519	1.00[CEU][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs12708520	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12909863	0.84[EUR][1000 genomes]
rs12910672	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12911229	0.91[ASN][1000 genomes]
rs13380103	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13737	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28610581	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs28623700	0.87[EUR][1000 genomes]
rs28693593	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs28783769	0.87[EUR][1000 genomes]
rs4075522	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4299117	1.00[CEU][hapmap]
rs4322627	0.80[EUR][1000 genomes]
rs4371118	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4393535	0.82[EUR][1000 genomes]
rs4451914	1.00[CEU][hapmap]
rs4545784	1.00[CEU][hapmap]
rs4886443	1.00[CEU][hapmap]
rs4886446	1.00[CEU][hapmap]
rs4886450	0.92[ASN][1000 genomes]
rs4886703	1.00[CEU][hapmap]
rs4886707	1.00[CEU][hapmap]
rs4886708	0.94[CEU][hapmap]
rs4886715	0.84[EUR][1000 genomes]
rs4886716	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4886718	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4886719	0.90[ASN][1000 genomes]
rs4886720	0.90[ASN][1000 genomes]
rs4886722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60972074	0.84[EUR][1000 genomes]
rs62027181	0.84[EUR][1000 genomes]
rs62027209	0.84[EUR][1000 genomes]
rs6495182	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7163451	0.87[EUR][1000 genomes]
rs7163907	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7166281	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7170787	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7175223	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7180574	0.80[EUR][1000 genomes]
rs7184046	1.00[CEU][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes]
rs8023268	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs8023495	0.85[ASN][1000 genomes]
rs8023815	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs8024244	0.80[EUR][1000 genomes]
rs8026113	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8029112	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs8030802	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs8034317	1.00[CEU][hapmap]
rs8036758	0.80[EUR][1000 genomes]
rs8036884	0.88[EUR][1000 genomes]
rs8037089	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8038760	1.00[CEU][hapmap]
rs8042772	0.90[ASN][1000 genomes]
rs9920028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920034	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
6	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
7	nsv531902	chr15:75724505-75919237	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
8	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
9	esv1813854	chr15:75898640-76002392	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs9944207	MAN2C1	cis	Heart Left Ventricle	GTEx
rs9944207	MAN2C1	cis	Thyroid	GTEx
rs9944207	SNUPN	cis	Whole Blood	GTEx
rs9944207	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs9944207	MAN2C1	cis	Stomach	GTEx
rs9944207	MAN2C1	cis	Artery Tibial	GTEx
rs9944207	MAN2C1	cis	Adipose Subcutaneous	GTEx
rs9944207	MAN2C1	cis	Nerve Tibial	GTEx
rs9944207	MAN2C1	cis	Esophagus Mucosa	GTEx
rs9944207	MAN2C1	cis	Artery Aorta	GTEx
rs9944207	MAN2C1	cis	Esophagus Muscularis	GTEx
rs9944207	MAN2C1	cis	lung	GTEx
rs9944207	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs9944207	MAN2C1	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75889400-75917600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:75889800-75917600	Weak transcription	Fetal Heart	heart
3	chr15:75890600-75917000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:75891000-75917200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:75892000-75913200	Strong transcription	Liver	Liver
6	chr15:75894800-75913400	Strong transcription	Fetal Intestine Large	intestine
7	chr15:75896000-75913400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:75896400-75913400	Strong transcription	Fetal Intestine Small	intestine
9	chr15:75896800-75913400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:75897000-75913000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:75897000-75914000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:75897800-75913400	Strong transcription	Fetal Brain Female	brain
13	chr15:75902000-75913000	Weak transcription	Small Intestine	intestine
14	chr15:75903000-75917600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:75904000-75913400	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:75904400-75913600	Strong transcription	Dnd41	blood
17	chr15:75904600-75913000	Strong transcription	GM12878-XiMat	blood
18	chr15:75904600-75913200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:75904600-75913400	Strong transcription	Primary B cells from peripheral blood	blood
20	chr15:75904600-75913600	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:75904600-75913600	Strong transcription	Fetal Lung	lung
22	chr15:75904800-75913400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:75904800-75913400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:75904800-75913400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:75904800-75913400	Strong transcription	Brain Germinal Matrix	brain
26	chr15:75905400-75913000	Strong transcription	Brain Anterior Caudate	brain
27	chr15:75907600-75913400	Strong transcription	Brain Hippocampus Middle	brain
28	chr15:75908400-75913200	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr15:75908600-75913400	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr15:75909400-75917200	Weak transcription	Psoas Muscle	Psoas
31	chr15:75909600-75917000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:75909600-75917200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr15:75909600-75917200	Weak transcription	HepG2	liver
34	chr15:75909600-75917400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:75909800-75917000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr15:75909800-75917200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:75909800-75917200	Weak transcription	Pancreas	Pancrea
38	chr15:75910000-75917400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:75910200-75917600	Weak transcription	Gastric	stomach
40	chr15:75910800-75913400	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr15:75911000-75913400	Strong transcription	Brain Angular Gyrus	brain
42	chr15:75911400-75917000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr15:75911600-75913000	Strong transcription	Brain Substantia Nigra	brain
44	chr15:75911600-75913400	Genic enhancers	Colon Smooth Muscle	Colon
45	chr15:75911800-75913000	Genic enhancers	Fetal Stomach	stomach
46	chr15:75911800-75917000	Weak transcription	Right Ventricle	heart
47	chr15:75911800-75917600	Weak transcription	Fetal Brain Male	brain
48	chr15:75912000-75913600	Weak transcription	Placenta	Placenta
49	chr15:75912000-75917600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr15:75912200-75914000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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