Variant report

Variant	rs2897358
Chromosome Location	chr7:100088640-100088641
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:100080163..100084843-chr7:100085212..100090254,7	MCF-7	breast:
2	chr7:100079431..100084153-chr7:100084209..100089579,10	K562	blood:

Variant related genes	Relation type
ENSG00000166924	Chromatin interaction
ENSG00000266372	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 42 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1073	1.00[ASN][1000 genomes]
rs11559117	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760536	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11761624	1.00[ASN][1000 genomes]
rs11761725	1.00[ASN][1000 genomes]
rs11761784	1.00[ASN][1000 genomes]
rs11763511	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764818	1.00[ASN][1000 genomes]
rs11766202	1.00[ASN][1000 genomes]
rs11766752	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769700	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772580	1.00[ASN][1000 genomes]
rs11773661	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962269	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406253	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406255	1.00[ASN][1000 genomes]
rs28629346	1.00[ASN][1000 genomes]
rs34989573	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074838	1.00[ASN][1000 genomes]
rs4385401	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4463351	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4469386	1.00[ASN][1000 genomes]
rs4472444	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4989959	1.00[ASN][1000 genomes]
rs60257855	1.00[ASN][1000 genomes]
rs60478351	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60644673	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60844404	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66648318	1.00[ASN][1000 genomes]
rs66958101	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67040465	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67196635	1.00[ASN][1000 genomes]
rs67239991	1.00[ASN][1000 genomes]
rs67483801	1.00[ASN][1000 genomes]
rs67885733	1.00[ASN][1000 genomes]
rs6948699	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953107	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955362	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6962151	1.00[ASN][1000 genomes]
rs6972167	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6974286	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975514	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975729	1.00[ASN][1000 genomes]
rs6978739	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979335	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73405353	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787620	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787825	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794485	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800667	1.00[ASN][1000 genomes]
rs7809801	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811142	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
2	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
3	nsv831071	chr7:99918025-100113413	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	287 gene(s)	inside rSNPs	diseases
4	nsv888776	chr7:100014711-100198386	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
5	nsv888777	chr7:100014711-100221867	Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
6	nsv888778	chr7:100014711-100236593	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	310 gene(s)	inside rSNPs	diseases
7	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
8	nsv888780	chr7:100032665-100198386	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
9	nsv527050	chr7:100056166-100125975	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv888781	chr7:100060928-100097895	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	nsv888782	chr7:100064719-100236593	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
12	nsv888783	chr7:100073292-100136241	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv888784	chr7:100076614-100097895	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:42)

SNP	Gene	Cis/trans	Tissue	Source
rs2897358	PILRA	cis	Muscle Skeletal	GTEx
rs2897358	PILRA	cis	Artery Tibial	GTEx
rs2897358	STAG3L5P	cis	Esophagus Mucosa	GTEx
rs2897358	PILRB	cis	Artery Tibial	GTEx
rs2897358	PVRIG2P	cis	Artery Tibial	GTEx
rs2897358	PILRA	cis	Artery Aorta	GTEx
rs2897358	PILRB	cis	Esophagus Mucosa	GTEx
rs2897358	PILRB	cis	Muscle Skeletal	GTEx
rs2897358	STAG3L5P	cis	Artery Aorta	GTEx
rs2897358	STAG3L5P	cis	lung	GTEx
rs2897358	PILRB	cis	Artery Aorta	GTEx
rs2897358	PILRA	cis	Esophagus Muscularis	GTEx
rs2897358	PILRA	cis	Nerve Tibial	GTEx
rs2897358	STAG3L5P	cis	Skin Sun Exposed Lower leg	GTEx
rs2897358	PILRB	cis	lung	GTEx
rs2897358	STAG3L5P	cis	Muscle Skeletal	GTEx
rs2897358	STAG3L5P	cis	Heart Left Ventricle	GTEx
rs2897358	STAG3L5P	cis	Adipose Subcutaneous	GTEx
rs2897358	PILRA	cis	Adipose Subcutaneous	GTEx
rs2897358	PILRB	cis	Thyroid	GTEx
rs2897358	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs2897358	PILRA	cis	Thyroid	GTEx
rs2897358	PILRA	cis	Skin Sun Exposed Lower leg	GTEx
rs2897358	STAG3L5P	cis	Artery Tibial	GTEx
rs2897358	PVRIG2P	cis	Thyroid	GTEx
rs2897358	PVRIG2P	cis	Esophagus Mucosa	GTEx
rs2897358	PILRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2897358	STAG3L5P	cis	Thyroid	GTEx
rs2897358	PILRB	cis	multi-tissue	Pritchard
rs2897358	PMS2P1	cis	Thyroid	GTEx
rs2897358	PVRIG2P	cis	lung	GTEx
rs2897358	PILRA	cis	Heart Left Ventricle	GTEx
rs2897358	PILRA	cis	Esophagus Mucosa	GTEx
rs2897358	PILRB	cis	Heart Left Ventricle	GTEx
rs2897358	PILRB	cis	Esophagus Muscularis	GTEx
rs2897358	PILRB	cis	Adipose Subcutaneous	GTEx
rs2897358	STAG3L5P	cis	Esophagus Muscularis	GTEx
rs2897358	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs2897358	PILRB	cis	Nerve Tibial	GTEx
rs2897358	PILRB	cis	Whole Blood	GTEx
rs2897358	STAG3L5P	cis	Stomach	GTEx
rs2897358	STAG3L5P	cis	Nerve Tibial	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100081000-100090600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr7:100081800-100091000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr7:100081800-100091000	Weak transcription	Right Atrium	heart
4	chr7:100082000-100090800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:100082200-100090600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr7:100082400-100088800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:100082600-100090400	Weak transcription	Stomach Mucosa	stomach
8	chr7:100082600-100090800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr7:100082600-100091000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:100082600-100091600	Weak transcription	Fetal Kidney	kidney
11	chr7:100083200-100091000	Weak transcription	Esophagus	oesophagus
12	chr7:100083600-100090600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr7:100083600-100090800	Weak transcription	Right Ventricle	heart
14	chr7:100083600-100091000	Weak transcription	Fetal Lung	lung
15	chr7:100083600-100091000	Weak transcription	NHDF-Ad	bronchial
16	chr7:100083600-100100800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr7:100084000-100091200	Weak transcription	Spleen	Spleen
18	chr7:100084200-100090400	Weak transcription	Adipose Nuclei	Adipose
19	chr7:100084400-100089200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr7:100085000-100091000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr7:100085200-100090000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr7:100085200-100090800	Weak transcription	K562	blood
23	chr7:100085600-100098000	Weak transcription	Hela-S3	cervix
24	chr7:100086200-100089200	Enhancers	Fetal Brain Male	brain
25	chr7:100087000-100091400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:100087200-100090200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:100087200-100091400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:100087400-100090400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr7:100087600-100090600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr7:100087600-100090600	Weak transcription	GM12878-XiMat	blood
31	chr7:100087600-100090800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr7:100087600-100090800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr7:100087800-100088800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr7:100087800-100090200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr7:100087800-100091000	Weak transcription	Ovary	ovary
36	chr7:100087800-100091200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr7:100088000-100088800	Weak transcription	Fetal Intestine Small	intestine
38	chr7:100088000-100089000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
39	chr7:100088000-100090000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr7:100088000-100091000	Weak transcription	Placenta	Placenta
41	chr7:100088200-100088800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:100088200-100088800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:100088200-100089000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:100088200-100090200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr7:100088200-100090400	Weak transcription	Fetal Muscle Leg	muscle
46	chr7:100088200-100091000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr7:100088400-100088800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr7:100088400-100089000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:100088400-100090000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr7:100088400-100090400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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