Variant report

Variant	rs1030484
Chromosome Location	chr5:76099912-76099913
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	chr5:76094082..76095930-chr5:76098926..76101541,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10053003	0.81[ASN][1000 genomes]
rs10067774	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12186639	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13157422	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13166089	0.86[ASN][1000 genomes]
rs13166450	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13177258	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13179180	0.87[ASN][1000 genomes]
rs13179405	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13180705	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1529505	0.85[CHD][hapmap]
rs1673073	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1963861	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2243003	0.85[CHD][hapmap]
rs2243010	0.84[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs2243022	0.85[CHD][hapmap]
rs2243057	0.85[CHD][hapmap]
rs2434656	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs250754	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs250765	0.82[EUR][1000 genomes]
rs3135471	0.87[ASN][1000 genomes]
rs34469953	0.86[ASN][1000 genomes]
rs3925483	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55925929	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56238109	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62365101	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62365102	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62365104	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62365105	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6453251	0.82[CHD][hapmap]
rs6453253	0.86[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs7712660	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv462213	chr5:76067624-76112869	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv598682	chr5:76067624-76112869	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1015997	chr5:76079720-76129241	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1031491	chr5:76083382-76129241	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2763908	chr5:76083394-76134777	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv598683	chr5:76086597-76129053	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv882210	chr5:76086597-76140337	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1022431	chr5:76086795-76127170	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1020397	chr5:76086795-76129241	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv598684	chr5:76086795-76130113	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription 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	4 gene(s)	inside rSNPs	diseases
12	nsv1025151	chr5:76086795-76134777	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1025061	chr5:76087544-76129241	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1033086	chr5:76088861-76129241	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1021460	chr5:76089512-76129241	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv1018194	chr5:76090951-76129241	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv521533	chr5:76092225-76100536	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv598685	chr5:76092225-76128521	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1030484	F2RL1	cis	multi-tissue	Pritchard
rs1030484	F2R	cis	Muscle Skeletal	GTEx
rs1030484	F2RL1	cis	Whole Blood	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:76088000-76100000	Weak transcription	HepG2	liver
2	chr5:76088200-76101400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:76091000-76101800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:76095000-76101400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:76097400-76100000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:76097400-76101400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:76097400-76101600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:76097600-76100000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:76097600-76101400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:76097800-76100400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:76097800-76101400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:76097800-76101400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:76097800-76101400	Weak transcription	NHDF-Ad	bronchial
14	chr5:76097800-76101600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:76098000-76100000	Enhancers	A549	lung
16	chr5:76098000-76100000	Weak transcription	Osteobl	bone
17	chr5:76098000-76100200	Weak transcription	HUVEC	blood vessel
18	chr5:76098000-76101400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr5:76098000-76101400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:76098000-76101400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:76098000-76101400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:76098000-76101400	Weak transcription	Hela-S3	cervix
23	chr5:76098000-76101400	Weak transcription	HSMMtube	muscle
24	chr5:76098000-76101400	Weak transcription	NHEK	skin
25	chr5:76098000-76101400	Weak transcription	NHLF	lung
26	chr5:76098000-76101600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:76098000-76104000	Weak transcription	Spleen	Spleen
28	chr5:76098000-76105000	Weak transcription	Right Atrium	heart
29	chr5:76098200-76101600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:76098200-76101600	Weak transcription	HMEC	breast
31	chr5:76098800-76100400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:76099400-76100000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:76099600-76101800	Weak transcription	Gastric	stomach
34	chr5:76099800-76100600	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr5:76099800-76100800	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr5:76099800-76100800	Enhancers	NH-A	brain
37	chr5:76099800-76102200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:76099800-76102600	Enhancers	Fetal Intestine Small	intestine
39	chr5:76099800-76103400	Enhancers	Fetal Intestine Large	intestine

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