Variant report

Variant	rs4545784
Chromosome Location	chr15:75755651-75755652
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75746593..75750755-chr15:75752145..75756687,6	MCF-7	breast:
2	chr15:75749224..75751066-chr15:75754223..75756445,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NEIL1-5	chr15:75755588-75756274	NONHSAT047347

Variant related genes	Relation type
ENSG00000169375	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10152155	0.84[EUR][1000 genomes]
rs10220738	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10775209	0.84[EUR][1000 genomes]
rs11072542	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11631052	0.83[EUR][1000 genomes]
rs11634863	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11636199	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs11637068	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11637586	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11638974	1.00[CEU][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11639183	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12708518	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12708519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12708520	1.00[CEU][hapmap];0.84[YRI][hapmap];0.83[EUR][1000 genomes]
rs12909863	0.83[EUR][1000 genomes]
rs12916964	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13380103	1.00[CEU][hapmap]
rs13737	0.89[CEU][hapmap]
rs28432989	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28610581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28693593	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs28737338	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28783769	0.88[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs3809547	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs4075522	1.00[CEU][hapmap]
rs4243033	0.83[EUR][1000 genomes]
rs4297648	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4299117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4322627	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4368141	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4381565	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4451914	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4462560	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs4486847	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4564532	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4886443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886446	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4886699	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4886700	0.84[EUR][1000 genomes]
rs4886703	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886708	0.94[CEU][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4886712	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4886715	0.83[EUR][1000 genomes]
rs4886716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4886722	1.00[CEU][hapmap]
rs5745920	0.84[EUR][1000 genomes]
rs60972074	0.81[EUR][1000 genomes]
rs62027181	0.82[EUR][1000 genomes]
rs6495171	0.95[JPT][hapmap]
rs6495182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7163907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs7166281	0.88[CEU][hapmap]
rs7166737	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7171507	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7175852	0.83[EUR][1000 genomes]
rs7176938	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7180574	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7184046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.80[EUR][1000 genomes]
rs7402293	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7402844	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7495610	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8023268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8023815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8024244	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8027365	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8027546	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8028277	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs8029112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8029394	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8030802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8034317	1.00[CEU][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8035987	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8036758	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8038760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9920028	1.00[CEU][hapmap]
rs9944207	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv482802	chr15:75686519-75899896	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	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
8	nsv904387	chr15:75706296-75806911	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	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
10	nsv904388	chr15:75730182-75804543	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised 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 miRNA target site	63 gene(s)	inside rSNPs	diseases
11	nsv904389	chr15:75739824-75806911	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4545784	MAN2C1	cis	Heart Left Ventricle	GTEx
rs4545784	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs4545784	MAN2C1	cis	Whole Blood	GTEx
rs4545784	SNUPN	cis	Thyroid	GTEx
rs4545784	MAN2C1	cis	Artery Tibial	GTEx
rs4545784	MAN2C1	cis	Nerve Tibial	GTEx
rs4545784	MAN2C1	cis	Artery Aorta	GTEx
rs4545784	MAN2C1	cis	lung	GTEx
rs4545784	MAN2C1	cis	Esophagus Mucosa	GTEx
rs4545784	MAN2C1	cis	Adipose Subcutaneous	GTEx
rs4545784	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs4545784	MAN2C1	cis	Esophagus Muscularis	GTEx
rs4545784	MAN2C1	cis	Thyroid	GTEx
rs4545784	MAN2C1	cis	Stomach	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75748600-75758200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:75748600-75759000	Weak transcription	Gastric	stomach
3	chr15:75748800-75757800	Weak transcription	Left Ventricle	heart
4	chr15:75748800-75758600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:75748800-75760000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:75748800-75760800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:75749000-75756800	Weak transcription	Primary T cells from cord blood	blood
8	chr15:75749000-75757200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:75749000-75758200	Weak transcription	Brain Hippocampus Middle	brain
10	chr15:75749000-75758200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:75749000-75758400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:75749000-75758600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:75749000-75758600	Weak transcription	Esophagus	oesophagus
14	chr15:75749000-75758600	Weak transcription	Right Ventricle	heart
15	chr15:75749000-75758800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:75749000-75759800	Weak transcription	Brain Substantia Nigra	brain
17	chr15:75749000-75760800	Weak transcription	Fetal Brain Male	brain
18	chr15:75749000-75761000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr15:75749000-75797800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr15:75749200-75755800	Weak transcription	Primary B cells from cord blood	blood
21	chr15:75749200-75756200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:75749200-75756200	Weak transcription	Fetal Stomach	stomach
23	chr15:75749200-75756600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:75749200-75756800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:75749200-75757400	Weak transcription	Thymus	Thymus
26	chr15:75749200-75757800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:75749200-75757800	Weak transcription	Brain Angular Gyrus	brain
28	chr15:75749200-75757800	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:75749200-75757800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:75749200-75757800	Weak transcription	HUVEC	blood vessel
31	chr15:75749200-75758000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:75749200-75758000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:75749200-75758000	Weak transcription	Lung	lung
34	chr15:75749200-75758000	Weak transcription	GM12878-XiMat	blood
35	chr15:75749200-75758200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:75749200-75758200	Weak transcription	Brain Anterior Caudate	brain
37	chr15:75749200-75758200	Weak transcription	Fetal Thymus	thymus
38	chr15:75749200-75758200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:75749200-75758400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:75749200-75758600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr15:75749200-75758800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr15:75749200-75759800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr15:75749200-75760000	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr15:75749200-75760600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr15:75749200-75760600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr15:75749200-75760800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr15:75749200-75776800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr15:75749200-75782000	Weak transcription	Right Atrium	heart
49	chr15:75749400-75756600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr15:75749400-75756800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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