Variant report

Variant	rs4526985
Chromosome Location	chr15:75686082-75686083
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75660349..75661908-chr15:75683928..75686715,2	MCF-7	breast:
2	chr15:75659605..75662163-chr15:75684611..75686539,2	K562	blood:
3	chr15:75659033..75662371-chr15:75684053..75687215,4	K562	blood:

Variant related genes	Relation type
ENSG00000140400	Chromatin interaction
ENSG00000260274	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10851882	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap]
rs11072544	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1128933	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11632105	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[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]
rs11632813	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11636031	0.89[GIH][hapmap]
rs11636199	0.84[CHD][hapmap];0.87[GIH][hapmap]
rs11637263	0.84[EUR][1000 genomes]
rs11638974	0.87[GIH][hapmap]
rs11853141	0.91[CHB][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs11855087	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs12324230	0.84[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12708519	0.89[GIH][hapmap]
rs12903362	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12911512	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12915221	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28610581	0.89[GIH][hapmap]
rs28693593	0.84[CHD][hapmap];0.87[GIH][hapmap]
rs28783769	0.84[GIH][hapmap]
rs3809549	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4075522	0.84[CHD][hapmap];0.87[GIH][hapmap]
rs4299117	0.89[GIH][hapmap]
rs4322627	0.89[GIH][hapmap]
rs4430707	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap]
rs4451914	0.89[CHD][hapmap];0.80[GIH][hapmap]
rs4886442	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886443	0.87[GIH][hapmap]
rs4886446	0.81[CHD][hapmap];0.89[GIH][hapmap]
rs4886699	0.87[CHD][hapmap];0.89[GIH][hapmap]
rs4886702	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4886703	0.89[CHD][hapmap];0.89[GIH][hapmap]
rs4886704	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]
rs4886705	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs4886706	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4886708	0.84[CHD][hapmap];0.89[GIH][hapmap]
rs6495172	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495173	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6495174	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs6495176	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6495178	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6495181	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6495182	0.89[GIH][hapmap]
rs7163783	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7163907	0.87[GIH][hapmap]
rs7164541	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7165292	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7165469	0.96[EUR][1000 genomes]
rs7166737	0.83[CHB][hapmap]
rs7170660	0.95[EUR][1000 genomes]
rs7173220	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7175139	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7175852	0.83[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap]
rs7182283	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs73436868	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8023815	0.89[GIH][hapmap]
rs8028277	0.87[CHD][hapmap];0.87[GIH][hapmap]
rs8029112	0.89[GIH][hapmap]
rs8030014	0.88[EUR][1000 genomes]
rs8030802	0.89[GIH][hapmap]
rs8034317	0.84[CHD][hapmap];0.89[GIH][hapmap]
rs8038760	0.80[GIH][hapmap]
rs9806241	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4526985	MAN2C1	cis	cerebellum	SCAN
rs4526985	RCN2	cis	cerebellum	SCAN
rs4526985	MAN2C1	cis	Nerve Tibial	GTEx
rs4526985	PSTPIP1	cis	parietal	SCAN
rs4526985	EDC3	cis	cerebellum	SCAN
rs4526985	SNUPN	cis	parietal	SCAN
rs4526985	MAN2C1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75662200-75699200	Strong transcription	Fetal Stomach	stomach
2	chr15:75662200-75715600	Strong transcription	Placenta	Placenta
3	chr15:75662400-75707600	Strong transcription	Primary T helper cells PMA-I stimulated	--
4	chr15:75662400-75717000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr15:75662400-75731400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:75662600-75695000	Strong transcription	Rectal Mucosa Donor 29	rectum
7	chr15:75662600-75707400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:75662600-75708000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:75662600-75708000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:75662600-75708600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:75662600-75722800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr15:75662800-75709400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:75662800-75723000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:75663000-75690400	Strong transcription	Hela-S3	cervix
15	chr15:75663000-75695200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:75663000-75707800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:75663000-75708000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:75663000-75708200	Strong transcription	Fetal Thymus	thymus
19	chr15:75663000-75708600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:75663000-75709400	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr15:75663000-75710000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr15:75663200-75689000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:75663200-75699600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:75663200-75706600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr15:75663200-75707800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr15:75663200-75707800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:75663400-75695400	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:75663400-75696600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr15:75663400-75707200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:75663400-75713000	Strong transcription	Thymus	Thymus
31	chr15:75663600-75689400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:75663600-75705600	Strong transcription	Left Ventricle	heart
33	chr15:75663600-75705600	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:75663600-75706400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:75663600-75707200	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr15:75663600-75707800	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr15:75663600-75708000	Strong transcription	Primary T cells from cord blood	blood
38	chr15:75664400-75708000	Strong transcription	Dnd41	blood
39	chr15:75664600-75702200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:75665800-75705400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:75665800-75723200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr15:75666800-75705400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr15:75670000-75689400	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr15:75671400-75690000	Strong transcription	Osteobl	bone
45	chr15:75671400-75694200	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr15:75671400-75705800	Strong transcription	Fetal Muscle Leg	muscle
47	chr15:75671400-75706400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:75671400-75708000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr15:75671400-75717800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:75671600-75690000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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