Variant report

Variant	rs4462560
Chromosome Location	chr15:75647964-75647965
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75647764-75648038	K562	blood:	n/a	n/a
2	POLR2A	chr15:75647557-75648080	K562	blood:	n/a	n/a
3	POLR2A	chr15:75645515-75647968	K562	blood:	n/a	n/a
4	POLR2A	chr15:75647920-75647969	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr15:75647665-75648032	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr15:75647659-75647990	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr15:75647499-75648037	GM12892	blood:	n/a	n/a
8	POLR2A	chr15:75647662-75648017	GM12878	blood:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75626851..75629633-chr15:75646566..75649228,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAN2C1-1	chr15:75647908-75648087	ENSG00000260591.1

No data

Variant related genes	Relation type
MIR631	TF binding region
ENSG00000140365	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 15 )

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

rs_ID	r²[population]
rs10152155	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10220738	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10775209	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10851882	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs11072542	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11072544	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1128933	0.83[CHB][hapmap]
rs11631052	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11632105	0.83[CHB][hapmap]
rs11632813	0.83[CHB][hapmap]
rs11634863	0.84[EUR][1000 genomes]
rs11636031	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs11636199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs11637068	0.89[EUR][1000 genomes]
rs11637586	0.81[EUR][1000 genomes]
rs11638974	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11855087	0.83[CHB][hapmap]
rs12324230	0.83[CHB][hapmap]
rs12708518	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12708519	1.00[CEU][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs12708520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs12916964	0.81[EUR][1000 genomes]
rs28432989	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28610581	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs28737338	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3809547	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3809549	0.83[CHB][hapmap]
rs4243033	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4297648	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4299117	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4322627	0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs4368141	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4451914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4486847	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4545784	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4564532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886443	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4886446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886700	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886702	0.83[CHB][hapmap]
rs4886703	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886704	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4886705	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4886706	0.83[CHB][hapmap]
rs4886707	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4886708	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886712	0.80[EUR][1000 genomes]
rs5745920	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6495174	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6495176	0.83[CHB][hapmap]
rs6495181	0.83[CHB][hapmap]
rs6495182	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7163907	1.00[CEU][hapmap]
rs7164541	0.83[CHB][hapmap]
rs7165469	0.80[ASN][1000 genomes]
rs7166737	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7171507	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7175852	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7176938	0.80[EUR][1000 genomes]
rs7180574	0.81[EUR][1000 genomes]
rs7182283	0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7402293	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7402844	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7495610	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8023268	1.00[CEU][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs8023815	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs8024244	0.81[EUR][1000 genomes]
rs8028182	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs8028277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8029112	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs8029394	0.90[EUR][1000 genomes]
rs8030014	0.83[ASN][1000 genomes]
rs8030802	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs8034317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8036758	0.81[EUR][1000 genomes]
rs8038760	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9806241	0.83[CHB][hapmap]

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	nsv1039713	chr15:75394213-75674389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv1037713	chr15:75401213-75665304	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv482859	chr15:75493899-75688451	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription 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	94 gene(s)	inside rSNPs	diseases
4	nsv1035829	chr15:75504534-75692417	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4462560	MAN2C1	cis	Stomach	GTEx
rs4462560	MAN2C1	cis	Esophagus Mucosa	GTEx
rs4462560	MAN2C1	cis	Thyroid	GTEx
rs4462560	MAN2C1	cis	Adipose Subcutaneous	GTEx
rs4462560	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs4462560	MAN2C1	cis	Nerve Tibial	GTEx
rs4462560	MAN2C1	cis	Esophagus Muscularis	GTEx
rs4462560	MAN2C1	cis	Artery Tibial	GTEx
rs4462560	MAN2C1	cis	Heart Left Ventricle	GTEx
rs4462560	MAN2C1	cis	Artery Aorta	GTEx
rs4462560	SNUPN	cis	Thyroid	GTEx
rs4462560	MAN2C1	cis	multi-tissue	Pritchard
rs4462560	MAN2C1	cis	Whole Blood	GTEx
rs4462560	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs4462560	MAN2C1	cis	lung	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75641200-75655000	Weak transcription	K562	blood
2	chr15:75641400-75648200	Weak transcription	Psoas Muscle	Psoas
3	chr15:75641400-75651200	Weak transcription	HSMM	muscle
4	chr15:75641400-75655400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:75641400-75658600	Weak transcription	HUVEC	blood vessel
6	chr15:75641600-75648200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr15:75641600-75648400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:75641600-75648400	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:75641600-75648400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:75641600-75648800	Weak transcription	Fetal Lung	lung
11	chr15:75641600-75650400	Weak transcription	Brain Substantia Nigra	brain
12	chr15:75641600-75654200	Weak transcription	Small Intestine	intestine
13	chr15:75641600-75659200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:75641600-75659600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:75641800-75648200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:75641800-75648800	Weak transcription	HMEC	breast
17	chr15:75641800-75651400	Weak transcription	Stomach Mucosa	stomach
18	chr15:75641800-75659600	Weak transcription	Fetal Heart	heart
19	chr15:75642000-75659600	Strong transcription	Fetal Intestine Small	intestine
20	chr15:75642200-75659800	Weak transcription	Fetal Brain Male	brain
21	chr15:75642400-75649000	Weak transcription	Osteobl	bone
22	chr15:75642400-75659800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:75642600-75648600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:75642800-75650400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr15:75642800-75654000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:75643000-75648600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:75643000-75659600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:75643200-75648400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:75643200-75649000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr15:75643200-75649200	Weak transcription	GM12878-XiMat	blood
31	chr15:75643200-75659800	Weak transcription	Right Atrium	heart
32	chr15:75643400-75648400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr15:75643400-75654400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr15:75643400-75656800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr15:75643600-75648400	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr15:75643600-75648800	Weak transcription	NH-A	brain
37	chr15:75643600-75656200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr15:75643800-75648000	Weak transcription	Dnd41	blood
39	chr15:75643800-75648200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:75643800-75657000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:75644000-75648800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr15:75644000-75650400	Weak transcription	HSMMtube	muscle
43	chr15:75644000-75651000	Weak transcription	Primary B cells from cord blood	blood
44	chr15:75644200-75659600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr15:75644200-75659800	Strong transcription	Fetal Stomach	stomach
46	chr15:75644400-75657600	Strong transcription	Gastric	stomach
47	chr15:75644400-75658000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr15:75644400-75658800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:75644400-75659600	Strong transcription	Colonic Mucosa	Colon
50	chr15:75644400-75659600	Strong transcription	Duodenum Mucosa	Duodenum

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