Variant report

Variant	rs4368141
Chromosome Location	chr15:75681000-75681001
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75659308..75663624-chr15:75678074..75682949,5	MCF-7	breast:
2	chr15:75659062..75661181-chr15:75680479..75684245,3	MCF-7	breast:
3	chr15:75659279..75662047-chr15:75680944..75683813,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NEIL1-3	chr15:75680608-75681169	NONHSAT047344

Variant related genes	Relation type
ENSG00000140400	Chromatin interaction
ENSG00000260274	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10152155	0.91[EUR][1000 genomes]
rs10220738	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10775209	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10851882	0.89[GIH][hapmap]
rs11072542	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1128933	0.89[GIH][hapmap]
rs11631052	0.93[EUR][1000 genomes]
rs11632105	0.87[GIH][hapmap]
rs11632813	0.87[GIH][hapmap]
rs11634863	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11636031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs11636199	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs11637068	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11637586	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11638974	1.00[CEU][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap]
rs12324230	0.87[GIH][hapmap]
rs12708518	0.83[EUR][1000 genomes]
rs12708519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs12708520	1.00[CEU][hapmap]
rs12916964	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13380103	1.00[CEU][hapmap]
rs28432989	0.80[EUR][1000 genomes]
rs28610581	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs28693593	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs28737338	0.84[EUR][1000 genomes]
rs28783769	0.88[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap]
rs3809547	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3809549	0.89[GIH][hapmap]
rs4075522	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap]
rs4243033	0.92[EUR][1000 genomes]
rs4297648	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4299117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4322627	0.94[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs4430707	0.89[GIH][hapmap]
rs4451914	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4462560	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4486847	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4526985	0.87[GIH][hapmap]
rs4545784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4564532	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4886443	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886446	0.83[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.84[EUR][1000 genomes]
rs4886699	0.89[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4886700	0.91[EUR][1000 genomes]
rs4886702	0.87[GIH][hapmap]
rs4886703	0.89[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4886704	0.87[GIH][hapmap]
rs4886707	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886708	0.83[ASW][hapmap];0.94[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs4886712	0.83[EUR][1000 genomes]
rs4886716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs5745920	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495171	0.95[JPT][hapmap]
rs6495174	0.87[GIH][hapmap]
rs6495176	0.87[GIH][hapmap]
rs6495181	0.87[GIH][hapmap]
rs6495182	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs7163907	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap]
rs7164541	0.87[GIH][hapmap]
rs7166737	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7171507	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7175852	0.83[ASW][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs7176938	0.82[EUR][1000 genomes]
rs7180574	0.84[EUR][1000 genomes]
rs7182283	0.87[GIH][hapmap]
rs7184046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7402293	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7402844	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7495610	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8023268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs8023815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs8024244	0.84[EUR][1000 genomes]
rs8028182	0.83[ASW][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs8028277	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8029112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs8029394	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8030802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs8034317	0.83[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.85[EUR][1000 genomes]
rs8035987	0.81[EUR][1000 genomes]
rs8036758	0.84[EUR][1000 genomes]
rs8038760	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9806241	0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv525265	chr15:75670079-75692303	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4368141	MAN2C1	cis	multi-tissue	Pritchard
rs4368141	SNUPN	cis	lymphoblastoid	seeQTL
rs4368141	MAN2C1	cis	parietal	SCAN
rs4368141	MAN2C1	cis	cerebellum	SCAN
rs4368141	ARID3B	cis	parietal	SCAN

Chromatin state (count:128 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75661600-75682200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:75662200-75699200	Strong transcription	Fetal Stomach	stomach
3	chr15:75662200-75715600	Strong transcription	Placenta	Placenta
4	chr15:75662400-75707600	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr15:75662400-75717000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:75662400-75731400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:75662600-75695000	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr15:75662600-75707400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:75662600-75708000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:75662600-75708000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:75662600-75708600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr15:75662600-75722800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr15:75662800-75682000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:75662800-75709400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:75662800-75723000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:75663000-75690400	Strong transcription	Hela-S3	cervix
17	chr15:75663000-75695200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:75663000-75707800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:75663000-75708000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:75663000-75708200	Strong transcription	Fetal Thymus	thymus
21	chr15:75663000-75708600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:75663000-75709400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr15:75663000-75710000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr15:75663200-75683200	Strong transcription	Adipose Nuclei	Adipose
25	chr15:75663200-75689000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:75663200-75699600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:75663200-75706600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr15:75663200-75707800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr15:75663200-75707800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:75663400-75682000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:75663400-75683400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:75663400-75695400	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr15:75663400-75696600	Strong transcription	Stomach Smooth Muscle	stomach
34	chr15:75663400-75707200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr15:75663400-75713000	Strong transcription	Thymus	Thymus
36	chr15:75663600-75682800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:75663600-75689400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:75663600-75705600	Strong transcription	Left Ventricle	heart
39	chr15:75663600-75705600	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:75663600-75706400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:75663600-75707200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr15:75663600-75707800	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr15:75663600-75708000	Strong transcription	Primary T cells from cord blood	blood
44	chr15:75663800-75682600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:75664400-75708000	Strong transcription	Dnd41	blood
46	chr15:75664600-75702200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:75665400-75683800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr15:75665800-75705400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:75665800-75723200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:75666800-75705400	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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