Variant report

Variant	rs3955236
Chromosome Location	chr9:21190833-21190834
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IFNA4-1	chr9:21190653-21191243	NONHSAT130373

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10116540	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10124609	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10738591	1.00[CEU][hapmap]
rs10757199	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs10811489	0.86[EUR][1000 genomes]
rs10811497	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10811508	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10811509	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10811514	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10964871	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap]
rs10964878	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10964884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10964885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10964896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs10964918	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10964920	1.00[CEU][hapmap]
rs10964928	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10964929	0.84[EUR][1000 genomes]
rs10964930	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10964932	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10964933	0.88[EUR][1000 genomes]
rs10964934	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10964943	0.83[EUR][1000 genomes]
rs10964957	0.94[CEU][hapmap]
rs12345537	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12551190	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12552812	0.86[EUR][1000 genomes]
rs12553763	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12555631	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs12555749	0.93[EUR][1000 genomes]
rs1330314	0.93[CEU][hapmap]
rs1411436	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1424854	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs1820313	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1831391	1.00[CEU][hapmap]
rs1834247	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs1854700	1.00[CEU][hapmap]
rs1928854	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1928855	0.87[EUR][1000 genomes]
rs1928856	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2007448	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2015345	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs2098814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs2383182	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs28437205	0.87[EUR][1000 genomes]
rs2939	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2990140	0.84[CEU][hapmap]
rs3750479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3758236	0.94[CEU][hapmap]
rs3855766	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4007646	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4112794	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4582643	0.93[CEU][hapmap]
rs4628333	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4977682	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4977684	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs56035072	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57122438	0.88[EUR][1000 genomes]
rs57146220	0.88[EUR][1000 genomes]
rs596180	0.86[CEU][hapmap]
rs604762	0.81[CEU][hapmap]
rs612966	0.88[CEU][hapmap]
rs614541	0.93[CEU][hapmap]
rs637949	0.86[CEU][hapmap]
rs6475510	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7019617	1.00[CEU][hapmap]
rs7019739	1.00[CEU][hapmap]
rs7022016	0.86[EUR][1000 genomes]
rs7030705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs7031048	0.93[CEU][hapmap]
rs7033839	1.00[CEU][hapmap]
rs7035639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7037147	1.00[CEU][hapmap]
rs7041635	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7043560	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7046898	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7047240	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7047351	0.91[EUR][1000 genomes]
rs7047805	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7047811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73418252	0.87[EUR][1000 genomes]
rs768848	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs768849	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7848803	0.87[EUR][1000 genomes]
rs7849623	1.00[CEU][hapmap]
rs7849862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7852323	0.84[EUR][1000 genomes]
rs7852809	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7854247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7856345	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7857863	0.86[EUR][1000 genomes]
rs7866359	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs980639	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817218	chr9:20687769-21309177	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv892724	chr9:20690244-21517302	Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
3	nsv466293	chr9:21029330-21199680	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv613752	chr9:21029330-21199680	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1032466	chr9:21052069-21243756	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv540084	chr9:21052069-21243756	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv892734	chr9:21108817-21323089	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv892735	chr9:21157373-21242161	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv968599	chr9:21166047-21239960	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv613755	chr9:21170364-21216028	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1016978	chr9:21171267-21214877	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1022579	chr9:21178517-21228248	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island lncRNA	8 gene(s)	inside rSNPs	diseases
13	esv2757324	chr9:21181454-21196515	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
14	esv2759678	chr9:21181454-21196515	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1018561	chr9:21181454-21228248	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv3325686	chr9:21182087-21194435	Enhancers	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
17	esv1795305	chr9:21183675-21205399	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1033177	chr9:21184475-21206426	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
19	esv3439842	chr9:21186801-21227493	Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv613756	chr9:21187700-21227391	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv438096	chr9:21190827-21199680	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3955236	KLHL9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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