Variant report

Variant	rs6495174
Chromosome Location	chr15:75712481-75712482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75659332..75663338-chr15:75710049..75712497,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260274	Chromatin interaction
ENSG00000140400	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10152155	0.89[ASN][1000 genomes]
rs10851882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.84[ASN][1000 genomes]
rs11072544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11072552	0.96[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap]
rs1128933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs11631052	0.83[ASN][1000 genomes]
rs11632105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap]
rs11632813	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs11636031	0.89[GIH][hapmap]
rs11636199	0.83[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs11637263	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11638974	0.83[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap]
rs11853141	0.87[CHB][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs11855087	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12324230	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs12708518	0.83[ASN][1000 genomes]
rs12708519	0.89[GIH][hapmap]
rs12708520	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs12903362	0.85[EUR][1000 genomes]
rs12911512	0.84[EUR][1000 genomes]
rs12915221	0.96[EUR][1000 genomes]
rs12916256	0.81[ASN][1000 genomes]
rs13380103	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs28432989	0.86[ASN][1000 genomes]
rs28610581	0.89[GIH][hapmap]
rs28693593	0.83[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.90[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];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs4075522	0.83[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap]
rs4243033	0.87[ASN][1000 genomes]
rs4297648	0.92[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];0.95[TSI][hapmap]
rs4451914	0.83[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4462560	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4486847	0.92[ASN][1000 genomes]
rs4526985	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]
rs4564532	0.83[CHB][hapmap];1.00[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];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4886699	0.83[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.86[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];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886703	0.83[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4886704	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]
rs4886705	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886706	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs4886708	0.83[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6495172	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6495173	0.95[EUR][1000 genomes]
rs6495176	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6495178	0.83[EUR][1000 genomes]
rs6495181	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes]
rs6495182	0.89[GIH][hapmap]
rs7163783	0.95[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];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs7165292	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7165469	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166737	0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7170660	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173220	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7175139	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7175852	0.83[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7176989	0.80[ASN][1000 genomes]
rs7182283	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73436868	0.84[EUR][1000 genomes]
rs8023815	0.89[GIH][hapmap]
rs8028277	0.83[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs8029112	0.89[GIH][hapmap]
rs8030014	0.90[EUR][1000 genomes]
rs8030802	0.89[GIH][hapmap]
rs8034317	0.83[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs8038760	0.80[GIH][hapmap]
rs9806241	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.85[EUR][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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6495174	MAN2C1	cis	multi-tissue	Pritchard
rs6495174	SNUPN	cis	parietal	SCAN
rs6495174	EDC3	cis	cerebellum	SCAN
rs6495174	PSTPIP1	cis	parietal	SCAN
rs6495174	MAN2C1	cis	Nerve Tibial	GTEx
rs6495174	MAN2C1	cis	cerebellum	SCAN
rs6495174	RCN2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75662200-75715600	Strong transcription	Placenta	Placenta
2	chr15:75662400-75717000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr15:75662400-75731400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:75662600-75722800	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr15:75662800-75723000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:75663400-75713000	Strong transcription	Thymus	Thymus
7	chr15:75665800-75723200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr15:75671400-75717800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:75683000-75730200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:75684400-75717800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:75690400-75715600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:75703200-75715000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:75703200-75732200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr15:75704200-75714400	Weak transcription	Small Intestine	intestine
15	chr15:75704200-75714800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:75704800-75713200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:75704800-75728200	Weak transcription	Psoas Muscle	Psoas
18	chr15:75704800-75742200	Weak transcription	Fetal Brain Male	brain
19	chr15:75705200-75713000	Weak transcription	NH-A	brain
20	chr15:75705200-75714200	Weak transcription	Brain Substantia Nigra	brain
21	chr15:75705200-75738200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:75705400-75712600	Weak transcription	Adipose Nuclei	Adipose
23	chr15:75705400-75712600	Weak transcription	Colon Smooth Muscle	Colon
24	chr15:75705400-75713200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr15:75705400-75713200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr15:75705400-75713200	Weak transcription	Brain Germinal Matrix	brain
27	chr15:75705400-75713800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:75705400-75714000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:75705400-75714200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr15:75705400-75714200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr15:75705400-75714200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:75705400-75714200	Weak transcription	HSMMtube	muscle
33	chr15:75705400-75714400	Weak transcription	Colonic Mucosa	Colon
34	chr15:75705400-75714400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr15:75705400-75714400	Weak transcription	Spleen	Spleen
36	chr15:75705400-75714800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:75705400-75714800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr15:75705400-75714800	Weak transcription	Pancreas	Pancrea
39	chr15:75705400-75714800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr15:75705400-75718400	Weak transcription	Brain Hippocampus Middle	brain
41	chr15:75705400-75720600	Weak transcription	Aorta	Aorta
42	chr15:75705400-75722600	Weak transcription	Gastric	stomach
43	chr15:75705400-75724600	Weak transcription	Fetal Heart	heart
44	chr15:75705400-75741000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr15:75705400-75742200	Weak transcription	Right Ventricle	heart
46	chr15:75705600-75714400	Weak transcription	Left Ventricle	heart
47	chr15:75705600-75715000	Weak transcription	Esophagus	oesophagus
48	chr15:75705600-75720400	Weak transcription	Brain Angular Gyrus	brain
49	chr15:75705800-75714200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr15:75705800-75714400	Weak transcription	Lung	lung

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