Variant report

Variant	rs4886702
Chromosome Location	chr15:75724703-75724704
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75724000..75726359-chr15:75746224..75748084,2	MCF-7	breast:
2	chr15:75722681..75724992-chr15:75746228..75748830,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169375	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10851882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap]
rs11072544	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs11072552	0.96[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs1128933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11632105	1.00[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];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];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11634402	0.96[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap]
rs11636031	0.89[GIH][hapmap]
rs11636199	0.83[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap]
rs11637263	0.88[EUR][1000 genomes]
rs11638974	0.83[CHB][hapmap];0.87[GIH][hapmap]
rs11853141	0.87[CHB][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs11855087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap]
rs12324230	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12708519	0.89[GIH][hapmap]
rs12708520	0.83[CHB][hapmap]
rs12903362	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12909709	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12911512	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12915221	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13380103	0.83[CHB][hapmap]
rs28610581	0.89[GIH][hapmap]
rs28693593	0.83[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap]
rs28783769	0.84[GIH][hapmap]
rs3809549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4075522	0.83[CHB][hapmap];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];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap]
rs4451914	0.83[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap]
rs4462560	0.83[CHB][hapmap]
rs4526985	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]
rs4564532	0.83[CHB][hapmap]
rs4886442	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886443	0.86[GIH][hapmap]
rs4886446	0.82[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap]
rs4886699	0.83[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap]
rs4886703	0.83[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap]
rs4886704	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]
rs4886705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4886706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886708	0.83[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap]
rs4886718	0.96[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap]
rs4886722	0.85[GIH][hapmap]
rs6495172	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495173	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6495174	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]
rs6495176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495178	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6495181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6495182	0.89[GIH][hapmap]
rs7163783	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7163907	0.87[GIH][hapmap]
rs7164541	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7165292	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7165469	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7166737	0.83[CHB][hapmap]
rs7170660	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7173220	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7175139	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7175852	0.83[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap]
rs7182283	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs73436868	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8023815	0.89[GIH][hapmap]
rs8028277	0.83[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap]
rs8029112	0.89[GIH][hapmap]
rs8030014	0.85[EUR][1000 genomes]
rs8030802	0.89[GIH][hapmap]
rs8034317	0.83[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap]
rs8038760	0.82[GIH][hapmap]
rs8043300	0.80[EUR][1000 genomes]
rs9806241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4886702	MAN2C1	cis	Nerve Tibial	GTEx
rs4886702	PSTPIP1	cis	parietal	SCAN
rs4886702	RCN2	cis	cerebellum	SCAN
rs4886702	MAN2C1	cis	cerebellum	SCAN
rs4886702	EDC3	cis	cerebellum	SCAN
rs4886702	SNUPN	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75662400-75731400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:75683000-75730200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:75703200-75732200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:75704800-75728200	Weak transcription	Psoas Muscle	Psoas
5	chr15:75704800-75742200	Weak transcription	Fetal Brain Male	brain
6	chr15:75705200-75738200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:75705400-75741000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:75705400-75742200	Weak transcription	Right Ventricle	heart
9	chr15:75708800-75740400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:75713200-75731600	Weak transcription	Stomach Mucosa	stomach
11	chr15:75715200-75735400	Weak transcription	Colonic Mucosa	Colon
12	chr15:75715400-75726200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:75715400-75741400	Weak transcription	Small Intestine	intestine
14	chr15:75715600-75742200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:75716200-75738200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:75717000-75742600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:75721200-75728000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr15:75721200-75739600	Weak transcription	Brain Substantia Nigra	brain
19	chr15:75721200-75742600	Weak transcription	Aorta	Aorta
20	chr15:75721800-75728200	Weak transcription	Esophagus	oesophagus
21	chr15:75721800-75735400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:75721800-75739600	Weak transcription	Brain Angular Gyrus	brain
23	chr15:75721800-75742000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:75722000-75741600	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:75722200-75738200	Weak transcription	Fetal Kidney	kidney
26	chr15:75722200-75742000	Weak transcription	Brain Cingulate Gyrus	brain
27	chr15:75722400-75726200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr15:75722400-75733400	Weak transcription	HUVEC	blood vessel
29	chr15:75722400-75735800	Weak transcription	NHDF-Ad	bronchial
30	chr15:75722600-75725600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr15:75722600-75741600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr15:75722600-75742000	Weak transcription	Brain Anterior Caudate	brain
33	chr15:75722800-75724800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr15:75722800-75725400	Weak transcription	Primary T cells from cord blood	blood
35	chr15:75722800-75725800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr15:75722800-75725800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:75722800-75725800	Weak transcription	Fetal Intestine Large	intestine
38	chr15:75722800-75726200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr15:75722800-75726200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:75722800-75726200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr15:75722800-75727400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:75722800-75727400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:75722800-75727400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:75722800-75727400	Weak transcription	Primary B cells from cord blood	blood
45	chr15:75722800-75727400	Weak transcription	Hela-S3	cervix
46	chr15:75722800-75727600	Weak transcription	Colon Smooth Muscle	Colon
47	chr15:75722800-75727600	Weak transcription	Fetal Stomach	stomach
48	chr15:75722800-75727600	Weak transcription	NHEK	skin
49	chr15:75722800-75727800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr15:75722800-75727800	Weak transcription	Adipose Nuclei	Adipose

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