Variant report

Variant	rs709668
Chromosome Location	chr5:96174186-96174187
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1230366	0.99[ASN][1000 genomes]
rs12519842	0.99[ASN][1000 genomes]
rs12659038	0.84[ASN][1000 genomes]
rs12659825	0.99[ASN][1000 genomes]
rs151823	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs151940	0.87[CHB][hapmap];0.80[ASN][1000 genomes]
rs152468	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.99[ASN][1000 genomes]
rs184971	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2042381	0.97[ASN][1000 genomes]
rs2351012	0.99[ASN][1000 genomes]
rs2351013	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs245472	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs246453	0.87[CHB][hapmap]
rs249960	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2545629	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2549804	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2549805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26491	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs26493	1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[ASN][1000 genomes]
rs26495	0.87[CHB][hapmap]
rs26496	0.86[CHB][hapmap]
rs26498	0.86[CHB][hapmap]
rs26510	0.86[CHB][hapmap]
rs26653	0.83[CHB][hapmap]
rs26654	0.86[CHB][hapmap]
rs27043	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs27044	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs27045	0.86[CHB][hapmap]
rs27432	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs27434	0.86[CHB][hapmap]
rs27529	0.86[CHB][hapmap]
rs27694	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27710	0.86[CHB][hapmap]
rs28119	0.87[CHB][hapmap]
rs2911138	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2911139	0.97[ASN][1000 genomes]
rs2927619	0.99[ASN][1000 genomes]
rs2927620	0.99[ASN][1000 genomes]
rs30186	0.87[CHB][hapmap]
rs30187	0.86[CHB][hapmap]
rs30376	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs30378	0.90[CHB][hapmap]
rs30379	0.87[CHB][hapmap]
rs30380	0.86[CHB][hapmap]
rs34735	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35134	0.84[YRI][hapmap]
rs39840	0.85[ASN][1000 genomes]
rs39841	0.84[ASN][1000 genomes]
rs3985002	0.99[ASN][1000 genomes]
rs42398	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs469758	0.91[CHB][hapmap]
rs469783	0.82[CHB][hapmap]
rs4869315	0.86[JPT][hapmap]
rs61112531	0.99[ASN][1000 genomes]
rs845028	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[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
rs709668	CAST	Cis_1M	lymphoblastoid	RTeQTL
rs709668	ERAP1	cis	lung	GTEx
rs709668	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96171600-96175000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:96171600-96175000	Weak transcription	Placenta	Placenta
3	chr5:96172000-96179200	Weak transcription	Fetal Thymus	thymus
4	chr5:96172200-96180400	Weak transcription	Thymus	Thymus
5	chr5:96172400-96174400	Weak transcription	GM12878-XiMat	blood
6	chr5:96172400-96178800	Weak transcription	Dnd41	blood
7	chr5:96173400-96174400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:96173400-96175400	Enhancers	Duodenum Mucosa	Duodenum
9	chr5:96173400-96175400	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr5:96173400-96177000	Enhancers	Fetal Intestine Large	intestine
11	chr5:96173600-96175800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:96173800-96174800	Weak transcription	Small Intestine	intestine
13	chr5:96173800-96175000	Enhancers	HUVEC	blood vessel
14	chr5:96173800-96175200	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr5:96173800-96175200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr5:96173800-96175600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:96174000-96174600	Enhancers	Colonic Mucosa	Colon
18	chr5:96174000-96176000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr5:96174000-96177400	Enhancers	Fetal Intestine Small	intestine

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