Variant report

Variant	rs7180574
Chromosome Location	chr15:75811599-75811600
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75744318..75747084-chr15:75809053..75812043,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10220738	0.83[EUR][1000 genomes]
rs10775209	0.82[EUR][1000 genomes]
rs11072542	0.82[EUR][1000 genomes]
rs11631052	0.81[EUR][1000 genomes]
rs11634863	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11636031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636199	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11637068	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11637586	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11638974	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11639183	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12708518	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12708519	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12708520	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12909863	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12916964	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13380103	0.84[EUR][1000 genomes]
rs28432989	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs28610581	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28623700	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs28693593	0.86[EUR][1000 genomes]
rs28737338	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28783769	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3809547	0.80[EUR][1000 genomes]
rs4075522	0.86[EUR][1000 genomes]
rs4243033	0.81[EUR][1000 genomes]
rs4297648	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4299117	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4322627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4368141	0.84[EUR][1000 genomes]
rs4381565	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4393535	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4451914	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4462560	0.81[EUR][1000 genomes]
rs4486847	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4545784	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4564532	0.84[EUR][1000 genomes]
rs4886443	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4886446	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4886699	0.84[EUR][1000 genomes]
rs4886703	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886707	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886708	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4886712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886715	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886716	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4886722	0.80[EUR][1000 genomes]
rs5745920	0.82[EUR][1000 genomes]
rs60972074	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62027181	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62027209	0.81[EUR][1000 genomes]
rs6495182	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163451	0.85[EUR][1000 genomes]
rs7163907	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7166737	0.82[EUR][1000 genomes]
rs7170787	0.82[EUR][1000 genomes]
rs7171507	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7175852	0.81[EUR][1000 genomes]
rs7176938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7184046	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7402293	0.82[EUR][1000 genomes]
rs7402844	0.83[EUR][1000 genomes]
rs7495610	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8023268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024244	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8027365	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8027546	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8028277	0.82[EUR][1000 genomes]
rs8029112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8029394	0.81[EUR][1000 genomes]
rs8030802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034317	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8035987	0.86[EUR][1000 genomes]
rs8036758	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8036884	0.86[EUR][1000 genomes]
rs8038760	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9944207	0.80[EUR][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	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	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
9	nsv904390	chr15:75795177-75840943	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7180574	MAN2C1	cis	Whole Blood	GTEx
rs7180574	MAN2C1	cis	Artery Tibial	GTEx
rs7180574	MAN2C1	cis	Esophagus Muscularis	GTEx
rs7180574	MAN2C1	cis	Esophagus Mucosa	GTEx
rs7180574	MAN2C1	cis	Heart Left Ventricle	GTEx
rs7180574	MAN2C1	cis	Skin Sun Exposed Lower leg	GTEx
rs7180574	MAN2C1	cis	lung	GTEx
rs7180574	MAN2C1	cis	Stomach	GTEx
rs7180574	MAN2C1	cis	Thyroid	GTEx
rs7180574	MAN2C1	cis	Artery Aorta	GTEx
rs7180574	SNUPN	Cis_1M	lymphoblastoid	RTeQTL
rs7180574	MAN2C1	cis	Nerve Tibial	GTEx
rs7180574	MAN2C1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75777200-75816800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:75777600-75812000	Weak transcription	Small Intestine	intestine
3	chr15:75780200-75812200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:75782600-75815200	Weak transcription	K562	blood
5	chr15:75785600-75814200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:75790000-75814200	Weak transcription	Psoas Muscle	Psoas
7	chr15:75797800-75819600	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr15:75797800-75819600	Strong transcription	Fetal Stomach	stomach
9	chr15:75797800-75820000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:75798400-75824800	Weak transcription	Stomach Mucosa	stomach
11	chr15:75798400-75825000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:75798600-75818800	Weak transcription	Fetal Heart	heart
13	chr15:75798800-75820400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:75799000-75813200	Weak transcription	Aorta	Aorta
15	chr15:75799200-75812800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr15:75799200-75814000	Weak transcription	Fetal Brain Male	brain
17	chr15:75799200-75814800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:75799400-75812200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr15:75799400-75814200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:75799400-75814200	Weak transcription	Pancreas	Pancrea
21	chr15:75799400-75818000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr15:75799400-75819400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:75799400-75821800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:75799600-75813200	Weak transcription	Esophagus	oesophagus
25	chr15:75799800-75812000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr15:75800600-75819800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:75801200-75812400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr15:75801400-75812200	Weak transcription	NHLF	lung
29	chr15:75801400-75820800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:75802400-75820000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:75802800-75819600	Strong transcription	Liver	Liver
32	chr15:75802800-75820000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:75803200-75816000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:75803200-75817800	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr15:75803200-75819800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr15:75803200-75828000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr15:75803400-75819600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr15:75803400-75820200	Strong transcription	Fetal Intestine Small	intestine
39	chr15:75803600-75817800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:75804000-75812200	Weak transcription	HMEC	breast
41	chr15:75804200-75816200	Strong transcription	Placenta	Placenta
42	chr15:75804400-75820000	Strong transcription	Fetal Muscle Leg	muscle
43	chr15:75804600-75816200	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:75804600-75816400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr15:75804600-75819600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:75804600-75819600	Strong transcription	Lung	lung
47	chr15:75804800-75820000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:75805200-75819800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr15:75805600-75812200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr15:75806400-75812200	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links