Variant report

Variant	rs7402844
Chromosome Location	chr15:75637396-75637397
allele	C/G
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	POLR2A	chr15:75637341-75638610	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75627029..75629352-chr15:75635997..75638161,2	MCF-7	breast:

Variant related genes	Relation type
NEIL1	TF binding region
ENSG00000140365	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10152155	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10220738	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10775209	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072542	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11631052	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11634863	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11636031	0.83[EUR][1000 genomes]
rs11637068	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11637586	0.82[EUR][1000 genomes]
rs12708518	0.82[EUR][1000 genomes]
rs12708519	0.83[EUR][1000 genomes]
rs12916964	0.82[EUR][1000 genomes]
rs28432989	0.81[EUR][1000 genomes]
rs28610581	0.83[EUR][1000 genomes]
rs28737338	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3809547	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4243033	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4297648	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4299117	0.82[EUR][1000 genomes]
rs4322627	0.83[EUR][1000 genomes]
rs4368141	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4451914	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4462560	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4486847	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4545784	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4564532	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4886443	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886446	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886699	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4886700	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4886703	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4886707	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4886708	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4886712	0.82[EUR][1000 genomes]
rs5745920	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6495182	0.83[EUR][1000 genomes]
rs7166737	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7171507	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7175852	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7176938	0.82[EUR][1000 genomes]
rs7180574	0.83[EUR][1000 genomes]
rs7402293	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7495610	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8023268	0.83[EUR][1000 genomes]
rs8023815	0.83[EUR][1000 genomes]
rs8024244	0.83[EUR][1000 genomes]
rs8028182	0.86[AFR][1000 genomes]
rs8028277	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8029112	0.83[EUR][1000 genomes]
rs8029394	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8030802	0.83[EUR][1000 genomes]
rs8034317	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8035987	0.80[EUR][1000 genomes]
rs8036758	0.83[EUR][1000 genomes]
rs8038760	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7402844	MAN2C1	cis	lung	GTEx
rs7402844	MAN2C1	cis	Nerve Tibial	GTEx
rs7402844	MAN2C1	cis	Whole Blood	GTEx
rs7402844	SNUPN	cis	Thyroid	GTEx
rs7402844	MAN2C1	cis	Thyroid	GTEx
rs7402844	MAN2C1	cis	Esophagus Mucosa	GTEx
rs7402844	MAN2C1	cis	Heart Left Ventricle	GTEx
rs7402844	MAN2C1	cis	Stomach	GTEx
rs7402844	MAN2C1	cis	Artery Aorta	GTEx
rs7402844	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs7402844	MAN2C1	cis	Adipose Subcutaneous	GTEx
rs7402844	MAN2C1	cis	Esophagus Muscularis	GTEx
rs7402844	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs7402844	MAN2C1	cis	Artery Tibial	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75629200-75638800	Weak transcription	Primary B cells from cord blood	blood
2	chr15:75629200-75639000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:75629200-75639000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr15:75629200-75639000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr15:75629200-75639200	Weak transcription	Aorta	Aorta
6	chr15:75629200-75639200	Weak transcription	Small Intestine	intestine
7	chr15:75629400-75637600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr15:75629400-75638400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr15:75629400-75638800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr15:75629400-75639000	Weak transcription	Brain Angular Gyrus	brain
11	chr15:75629400-75639000	Weak transcription	Colonic Mucosa	Colon
12	chr15:75629400-75639000	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:75629400-75639000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:75629400-75639200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:75629400-75639200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr15:75629400-75639200	Weak transcription	NH-A	brain
17	chr15:75629400-75639400	Weak transcription	HSMM	muscle
18	chr15:75629400-75639400	Weak transcription	NHDF-Ad	bronchial
19	chr15:75629600-75638600	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr15:75629600-75639000	Weak transcription	GM12878-XiMat	blood
21	chr15:75629600-75639000	Weak transcription	HepG2	liver
22	chr15:75629600-75639000	Weak transcription	HUVEC	blood vessel
23	chr15:75629600-75639600	Weak transcription	Hela-S3	cervix
24	chr15:75630400-75638200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr15:75631800-75639000	Weak transcription	Brain Anterior Caudate	brain
26	chr15:75632000-75639600	Weak transcription	HSMMtube	muscle
27	chr15:75632400-75639000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr15:75632400-75639200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr15:75632400-75639200	Weak transcription	Ovary	ovary
30	chr15:75632600-75638400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr15:75632600-75639000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:75632600-75639000	Weak transcription	Brain Substantia Nigra	brain
33	chr15:75632600-75639200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:75632600-75639200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:75632600-75639200	Weak transcription	Lung	lung
36	chr15:75632600-75639200	Weak transcription	HMEC	breast
37	chr15:75632600-75639400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr15:75632800-75639000	Weak transcription	NHEK	skin
39	chr15:75632800-75639200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:75632800-75639200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr15:75632800-75639200	Weak transcription	Right Ventricle	heart
42	chr15:75633000-75639200	Weak transcription	Esophagus	oesophagus
43	chr15:75633400-75638800	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr15:75633600-75637400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:75633600-75639000	Weak transcription	Primary T cells from cord blood	blood
46	chr15:75633600-75639000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr15:75633600-75639000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr15:75633600-75639200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:75633600-75639200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:75633600-75639400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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