Variant report

Variant	rs4886718
Chromosome Location	chr15:75915137-75915138
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75914032..75916451-chr15:75943041..75945387,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10163126	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10851882	0.96[CEU][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs11072552	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072553	0.82[ASN][1000 genomes]
rs11632105	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs11632813	0.92[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs11634402	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636031	0.82[GIH][hapmap]
rs11636199	0.85[GIH][hapmap]
rs11637263	0.80[EUR][1000 genomes]
rs11638974	0.80[GIH][hapmap]
rs11855087	0.96[CEU][hapmap]
rs11856606	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs12101874	0.94[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12324230	0.96[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs12708519	0.82[GIH][hapmap]
rs12903362	0.81[EUR][1000 genomes]
rs12909709	0.89[EUR][1000 genomes]
rs12910672	0.90[ASN][1000 genomes]
rs12911229	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12911512	0.82[EUR][1000 genomes]
rs12916256	0.90[EUR][1000 genomes]
rs13737	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs28376842	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28610581	0.82[GIH][hapmap]
rs28693593	0.84[GIH][hapmap]
rs28783769	0.84[GIH][hapmap]
rs4075522	0.85[GIH][hapmap]
rs4299117	0.82[GIH][hapmap]
rs4319732	0.90[EUR][1000 genomes]
rs4322627	0.82[GIH][hapmap]
rs4371118	0.94[ASN][1000 genomes]
rs4408507	0.80[EUR][1000 genomes]
rs4430707	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs4886446	0.82[GIH][hapmap]
rs4886449	0.90[EUR][1000 genomes]
rs4886450	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886452	0.92[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs4886702	0.96[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap]
rs4886703	0.82[GIH][hapmap]
rs4886704	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap]
rs4886705	0.96[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs4886706	0.96[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs4886708	0.82[GIH][hapmap]
rs4886719	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886720	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886722	0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6495176	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap]
rs6495178	0.81[EUR][1000 genomes]
rs6495181	0.96[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs6495182	0.82[GIH][hapmap]
rs7163907	0.85[GIH][hapmap]
rs7164541	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs7166281	0.90[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7170787	0.87[ASN][1000 genomes]
rs7175223	0.90[ASN][1000 genomes]
rs7176989	0.89[EUR][1000 genomes]
rs73436868	0.83[EUR][1000 genomes]
rs8023495	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8023815	0.82[GIH][hapmap]
rs8026113	0.94[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs8029112	0.82[GIH][hapmap]
rs8030802	0.82[GIH][hapmap]
rs8034317	0.82[GIH][hapmap]
rs8037089	0.91[ASN][1000 genomes]
rs8042772	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8043300	0.89[EUR][1000 genomes]
rs9806241	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs9920028	0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9944207	1.00[JPT][hapmap];0.92[ASN][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4886718	MAN2C1	cis	Whole Blood	GTEx
rs4886718	SNUPN	cis	lymphoblastoid	seeQTL
rs4886718	SNUPN	cis	parietal	SCAN
rs4886718	MAN2C1	cis	Nerve Tibial	GTEx
rs4886718	PSTPIP1	cis	parietal	SCAN
rs4886718	MAN2C1	cis	cerebellum	SCAN
rs4886718	GOLGA6C	cis	lymphoblastoid	seeQTL
rs4886718	RCN2	cis	cerebellum	SCAN

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	chr15:75903000-75917600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:75909400-75917200	Weak transcription	Psoas Muscle	Psoas
7	chr15:75909600-75917000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:75909600-75917200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr15:75909600-75917200	Weak transcription	HepG2	liver
10	chr15:75909600-75917400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:75909800-75917000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr15:75909800-75917200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:75909800-75917200	Weak transcription	Pancreas	Pancrea
14	chr15:75910000-75917400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:75910200-75917600	Weak transcription	Gastric	stomach
16	chr15:75911400-75917000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr15:75911800-75917000	Weak transcription	Right Ventricle	heart
18	chr15:75911800-75917600	Weak transcription	Fetal Brain Male	brain
19	chr15:75912000-75917600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:75912200-75917000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:75912600-75917000	Weak transcription	Colonic Mucosa	Colon
22	chr15:75912600-75917200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr15:75912800-75917000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:75913000-75915200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr15:75913000-75916600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr15:75913000-75917000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:75913000-75917000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr15:75913000-75917000	Weak transcription	K562	blood
29	chr15:75913000-75917200	Weak transcription	Lung	lung
30	chr15:75913200-75917000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr15:75913200-75917000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:75913200-75917200	Weak transcription	Liver	Liver
33	chr15:75913200-75917600	Weak transcription	Brain Substantia Nigra	brain
34	chr15:75913400-75915400	Enhancers	Fetal Thymus	thymus
35	chr15:75913400-75916600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr15:75913400-75916800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr15:75913400-75916800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr15:75913400-75917000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr15:75913400-75917000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:75913400-75917000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:75913400-75917000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr15:75913400-75917000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:75913400-75917000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:75913400-75917000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr15:75913400-75917000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:75913400-75917000	Weak transcription	Brain Angular Gyrus	brain
47	chr15:75913400-75917000	Weak transcription	Brain Hippocampus Middle	brain
48	chr15:75913400-75917000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:75913400-75917000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr15:75913400-75917000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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