Variant report

Variant	rs4886704
Chromosome Location	chr15:75732993-75732994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75731360..75733909-chr15:75745980..75748280,2	K562	blood:
2	chr15:75731585..75733520-chr15:75735552..75738402,2	K562	blood:
3	chr15:75729900..75734080-chr15:75744771..75746662,3	MCF-7	breast:
4	chr15:75660231..75661838-chr15:75732480..75735371,2	MCF-7	breast:
5	chr15:75729907..75733520-chr15:75735552..75738005,3	K562	blood:

Variant related genes	Relation type
ENSG00000169375	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000140400	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10152155	0.89[ASN][1000 genomes]
rs10851882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.83[ASN][1000 genomes]
rs11072544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11072552	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs1128933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs11631052	0.84[ASN][1000 genomes]
rs11632105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11632813	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11634402	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap]
rs11636031	0.89[GIH][hapmap]
rs11636199	0.83[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs11637263	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11638974	0.83[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap]
rs11853141	0.87[CHB][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs11855087	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12101874	0.88[CEU][hapmap]
rs12324230	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs12708518	0.82[ASN][1000 genomes]
rs12708519	0.89[GIH][hapmap]
rs12708520	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs12903362	0.88[EUR][1000 genomes]
rs12909709	0.80[EUR][1000 genomes]
rs12911512	0.87[EUR][1000 genomes]
rs12915221	0.92[EUR][1000 genomes]
rs12916256	0.80[ASN][1000 genomes]
rs13380103	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs28432989	0.85[ASN][1000 genomes]
rs28610581	0.89[GIH][hapmap]
rs28693593	0.83[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs28737338	0.85[ASN][1000 genomes]
rs28783769	0.84[GIH][hapmap]
rs3809549	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs4075522	0.83[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs4243033	0.86[ASN][1000 genomes]
rs4297648	0.93[ASN][1000 genomes]
rs4299117	0.89[GIH][hapmap]
rs4322627	0.89[GIH][hapmap]
rs4430707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap]
rs4451914	0.83[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4462560	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4486847	0.93[ASN][1000 genomes]
rs4526985	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs4564532	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4886442	0.93[EUR][1000 genomes]
rs4886443	0.87[GIH][hapmap]
rs4886446	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4886452	0.88[CEU][hapmap]
rs4886699	0.83[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4886700	0.89[ASN][1000 genomes]
rs4886702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886703	0.83[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4886705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886706	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs4886708	0.83[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4886718	0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap]
rs4886722	0.85[GIH][hapmap]
rs6495172	0.91[EUR][1000 genomes]
rs6495173	0.91[EUR][1000 genomes]
rs6495174	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495176	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6495178	0.86[EUR][1000 genomes]
rs6495181	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes]
rs6495182	0.89[GIH][hapmap]
rs7163783	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7163907	0.87[GIH][hapmap]
rs7164541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs7165292	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7165469	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7166737	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7170660	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7173220	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7175139	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7175852	0.83[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7182283	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73436868	0.86[EUR][1000 genomes]
rs8023815	0.89[GIH][hapmap]
rs8028277	0.83[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8029112	0.89[GIH][hapmap]
rs8030014	0.86[EUR][1000 genomes]
rs8030802	0.89[GIH][hapmap]
rs8034317	0.83[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8038760	0.80[GIH][hapmap]
rs8043300	0.80[EUR][1000 genomes]
rs9806241	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4886704	RCN2	cis	cerebellum	SCAN
rs4886704	EDC3	cis	cerebellum	SCAN
rs4886704	MAN2C1	cis	Nerve Tibial	GTEx
rs4886704	MAN2C1	cis	cerebellum	SCAN
rs4886704	PSTPIP1	cis	parietal	SCAN
rs4886704	SNUPN	cis	parietal	SCAN
rs4886704	MAN2C1	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75704800-75742200	Weak transcription	Fetal Brain Male	brain
2	chr15:75705200-75738200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:75705400-75741000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:75705400-75742200	Weak transcription	Right Ventricle	heart
5	chr15:75708800-75740400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:75715200-75735400	Weak transcription	Colonic Mucosa	Colon
7	chr15:75715400-75741400	Weak transcription	Small Intestine	intestine
8	chr15:75715600-75742200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr15:75716200-75738200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:75717000-75742600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:75721200-75739600	Weak transcription	Brain Substantia Nigra	brain
12	chr15:75721200-75742600	Weak transcription	Aorta	Aorta
13	chr15:75721800-75735400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:75721800-75739600	Weak transcription	Brain Angular Gyrus	brain
15	chr15:75721800-75742000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:75722000-75741600	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:75722200-75738200	Weak transcription	Fetal Kidney	kidney
18	chr15:75722200-75742000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:75722400-75733400	Weak transcription	HUVEC	blood vessel
20	chr15:75722400-75735800	Weak transcription	NHDF-Ad	bronchial
21	chr15:75722600-75741600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr15:75722600-75742000	Weak transcription	Brain Anterior Caudate	brain
23	chr15:75722800-75733800	Weak transcription	Thymus	Thymus
24	chr15:75722800-75734000	Weak transcription	Fetal Brain Female	brain
25	chr15:75722800-75734600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:75722800-75734600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr15:75722800-75734800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:75722800-75735400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:75722800-75735600	Weak transcription	Fetal Lung	lung
30	chr15:75722800-75735600	Weak transcription	NHLF	lung
31	chr15:75722800-75735800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:75722800-75735800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr15:75722800-75738200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:75722800-75738600	Weak transcription	Spleen	Spleen
35	chr15:75722800-75741000	Weak transcription	Brain Germinal Matrix	brain
36	chr15:75722800-75741400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr15:75722800-75741600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:75722800-75741600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr15:75722800-75742000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr15:75722800-75742200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr15:75722800-75742200	Weak transcription	Gastric	stomach
42	chr15:75722800-75742200	Weak transcription	Pancreas	Pancrea
43	chr15:75722800-75742200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr15:75722800-75742200	Weak transcription	HSMMtube	muscle
45	chr15:75723000-75735400	Weak transcription	Placenta	Placenta
46	chr15:75723000-75740200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr15:75723000-75742600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr15:75723800-75736200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:75724400-75735400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:75724600-75735200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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