Variant report

Variant	rs2549804
Chromosome Location	chr5:96175226-96175227
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1230366	1.00[ASN][1000 genomes]
rs12519842	1.00[ASN][1000 genomes]
rs12659038	0.84[ASN][1000 genomes]
rs12659825	1.00[ASN][1000 genomes]
rs151823	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs151940	0.87[CHB][hapmap]
rs152468	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs184971	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs187387	0.90[YRI][hapmap]
rs190298	0.90[YRI][hapmap]
rs2042381	0.97[ASN][1000 genomes]
rs2351012	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2351013	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs245472	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs246453	0.87[CHB][hapmap]
rs249960	0.97[ASN][1000 genomes]
rs2545629	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2549805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26491	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs26493	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs26495	0.87[CHB][hapmap]
rs26496	0.87[CHB][hapmap]
rs26498	0.87[CHB][hapmap]
rs26510	0.87[CHB][hapmap]
rs26654	0.82[CHB][hapmap]
rs27043	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs27044	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs27045	0.87[CHB][hapmap]
rs27432	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs27434	0.86[CHB][hapmap]
rs27529	0.87[CHB][hapmap]
rs27645	0.90[YRI][hapmap]
rs27694	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27710	0.87[CHB][hapmap]
rs28119	0.87[CHB][hapmap]
rs2911138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2911139	0.97[ASN][1000 genomes]
rs2927619	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2927620	1.00[ASN][1000 genomes]
rs30186	0.87[CHB][hapmap]
rs30187	0.87[CHB][hapmap]
rs30376	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs30378	0.91[CHB][hapmap]
rs30379	0.87[CHB][hapmap]
rs30380	0.87[CHB][hapmap]
rs34735	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34755	0.83[YRI][hapmap]
rs39840	0.84[ASN][1000 genomes]
rs39841	0.84[ASN][1000 genomes]
rs3985002	1.00[ASN][1000 genomes]
rs42398	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs469758	0.91[CHB][hapmap]
rs469783	0.83[CHB][hapmap]
rs4869315	0.86[JPT][hapmap]
rs61112531	1.00[ASN][1000 genomes]
rs709668	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs845028	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv830411	chr5:96045168-96187817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv516293	chr5:96070205-96216387	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv948703	chr5:96078309-96368839	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1027472	chr5:96081592-96337550	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1028741	chr5:96082401-96372165	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv949058	chr5:96082433-96390619	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv598963	chr5:96084776-96363407	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv432756	chr5:96113844-96234644	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv531967	chr5:96127842-96302702	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2549804	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs2549804	CAST	Cis_1M	lymphoblastoid	RTeQTL
rs2549804	ERAP1	cis	lung	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96172000-96179200	Weak transcription	Fetal Thymus	thymus
2	chr5:96172200-96180400	Weak transcription	Thymus	Thymus
3	chr5:96172400-96178800	Weak transcription	Dnd41	blood
4	chr5:96173400-96175400	Enhancers	Duodenum Mucosa	Duodenum
5	chr5:96173400-96175400	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr5:96173400-96177000	Enhancers	Fetal Intestine Large	intestine
7	chr5:96173600-96175800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:96173800-96175600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:96174000-96176000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr5:96174000-96177400	Enhancers	Fetal Intestine Small	intestine
11	chr5:96174400-96175600	Enhancers	NHEK	skin
12	chr5:96174800-96175400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:96174800-96175400	Enhancers	Small Intestine	intestine
14	chr5:96175000-96175400	Enhancers	Placenta	Placenta
15	chr5:96175000-96175600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr5:96175000-96175800	Enhancers	Primary hematopoietic stem cells	blood
17	chr5:96175000-96176000	Weak transcription	GM12878-XiMat	blood
18	chr5:96175200-96175400	Enhancers	Placenta Amnion	Placenta Amnion
19	chr5:96175200-96176800	Weak transcription	Psoas Muscle	Psoas
20	chr5:96175200-96179800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:96175200-96180000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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