Variant report

Variant	rs11558476
Chromosome Location	chr7:99654689-99654690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11558475	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531809	0.82[ASN][1000 genomes]
rs12532238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12673441	0.90[MEX][hapmap];0.93[MKK][hapmap];0.82[ASN][1000 genomes]
rs13238380	0.82[ASN][1000 genomes]
rs2261360	0.90[MEX][hapmap];0.86[MKK][hapmap]
rs2897075	0.82[ASN][1000 genomes]
rs35228488	0.82[ASN][1000 genomes]
rs4308665	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4421299	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4727445	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4729573	0.81[ASN][1000 genomes]
rs4729575	0.82[JPT][hapmap];0.86[MKK][hapmap]
rs55969052	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56054049	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60697181	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67091024	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67110214	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68038211	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963345	0.82[ASN][1000 genomes]
rs72615158	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72615159	0.82[ASN][1000 genomes]
rs73158411	0.81[ASN][1000 genomes]
rs7780686	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796006	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7803317	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs941289	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11558476	ZSCAN21	cis	multi-tissue	Pritchard
rs11558476	MBLAC1	cis	cerebellum	SCAN
rs11558476	AP4M1	cis	cerebellum	SCAN
rs11558476	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs11558476	MUC17	cis	parietal	SCAN
rs11558476	OR2AE1	cis	parietal	SCAN
rs11558476	MCM7	cis	parietal	SCAN
rs11558476	PILRB	cis	parietal	SCAN
rs11558476	LOC389541	Cis_1M	lymphoblastoid	RTeQTL
rs11558476	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs11558476	PILRB	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99648400-99654800	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr7:99648400-99654800	Weak transcription	Psoas Muscle	Psoas
3	chr7:99648400-99655000	Weak transcription	Primary B cells from cord blood	blood
4	chr7:99648400-99655000	Weak transcription	Fetal Kidney	kidney
5	chr7:99648400-99655000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:99648400-99655000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:99648400-99655000	Weak transcription	K562	blood
8	chr7:99648400-99655200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr7:99648400-99655400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:99648400-99655800	Weak transcription	Colonic Mucosa	Colon
11	chr7:99648400-99656200	Weak transcription	Hela-S3	cervix
12	chr7:99648400-99661400	Weak transcription	Small Intestine	intestine
13	chr7:99648400-99667600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:99648400-99667600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:99648400-99667600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr7:99648400-99667800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr7:99648400-99668000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr7:99648600-99654800	Weak transcription	Fetal Thymus	thymus
19	chr7:99648600-99655000	Weak transcription	HMEC	breast
20	chr7:99648600-99655200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr7:99648600-99656600	Weak transcription	Fetal Heart	heart
22	chr7:99648600-99656600	Weak transcription	GM12878-XiMat	blood
23	chr7:99648600-99656800	Weak transcription	NHDF-Ad	bronchial
24	chr7:99648600-99660600	Weak transcription	HSMM	muscle
25	chr7:99648600-99663400	Weak transcription	Stomach Mucosa	stomach
26	chr7:99649600-99655000	Weak transcription	HepG2	liver
27	chr7:99650800-99654800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr7:99651600-99655000	Weak transcription	Fetal Brain Male	brain
29	chr7:99652600-99659000	Strong transcription	Fetal Muscle Leg	muscle
30	chr7:99653400-99666400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:99653800-99658800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr7:99653800-99660200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr7:99653800-99663000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:99653800-99663200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:99653800-99664200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:99653800-99667600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr7:99654000-99657200	Strong transcription	Brain Substantia Nigra	brain
38	chr7:99654000-99658000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:99654000-99658000	Strong transcription	Fetal Intestine Large	intestine
40	chr7:99654000-99662200	Strong transcription	Fetal Stomach	stomach
41	chr7:99654000-99663600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr7:99654000-99663800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr7:99654000-99664000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:99654000-99668000	Strong transcription	Fetal Brain Female	brain
45	chr7:99654200-99656000	Strong transcription	Primary hematopoietic stem cells	blood
46	chr7:99654200-99656600	Strong transcription	Rectal Smooth Muscle	rectum
47	chr7:99654200-99663000	Strong transcription	Stomach Smooth Muscle	stomach
48	chr7:99654200-99663600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr7:99654200-99666400	Strong transcription	Fetal Intestine Small	intestine
50	chr7:99654200-99667400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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