Variant report

Variant	rs9844124
Chromosome Location	chr3:162429810-162429811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 141 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10936308	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11922500	0.85[EUR][1000 genomes]
rs11923566	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11925750	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11926186	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11926645	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12489679	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496550	0.88[ASN][1000 genomes]
rs12496594	0.82[ASN][1000 genomes]
rs12496614	0.93[ASN][1000 genomes]
rs12631404	0.91[ASN][1000 genomes]
rs12635779	0.91[ASN][1000 genomes]
rs13063582	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13063904	0.80[AFR][1000 genomes]
rs13069139	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13077716	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13083886	0.85[EUR][1000 genomes]
rs13085871	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13092433	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13092614	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13092643	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13093719	0.84[ASN][1000 genomes]
rs13094746	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1353556	0.93[ASN][1000 genomes]
rs1353557	0.93[ASN][1000 genomes]
rs1353558	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1390793	0.85[AFR][1000 genomes]
rs1566063	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs16851335	0.87[ASN][1000 genomes]
rs1874510	0.83[EUR][1000 genomes]
rs1874512	0.83[EUR][1000 genomes]
rs2029925	0.85[EUR][1000 genomes]
rs2173065	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2173066	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2173067	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2361609	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4858909	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4858911	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55807361	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56162745	0.91[ASN][1000 genomes]
rs56242739	0.87[EUR][1000 genomes]
rs56815734	0.91[ASN][1000 genomes]
rs57617609	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58194889	0.86[ASN][1000 genomes]
rs58604878	0.91[ASN][1000 genomes]
rs59027724	0.84[ASN][1000 genomes]
rs59307821	0.88[ASN][1000 genomes]
rs61170375	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62292528	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs62292532	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs62294571	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs62294573	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62294581	0.93[ASN][1000 genomes]
rs6414405	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6414407	0.87[EUR][1000 genomes]
rs6441540	0.85[EUR][1000 genomes]
rs6441541	0.85[EUR][1000 genomes]
rs6441542	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6441543	0.85[EUR][1000 genomes]
rs6441545	0.87[EUR][1000 genomes]
rs6441546	0.94[ASN][1000 genomes]
rs66614152	0.85[ASN][1000 genomes]
rs6764576	0.87[EUR][1000 genomes]
rs6775650	0.80[ASN][1000 genomes]
rs6777228	0.90[AFR][1000 genomes]
rs6778765	0.85[EUR][1000 genomes]
rs6798611	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6802045	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs73010393	0.91[ASN][1000 genomes]
rs73010394	0.91[ASN][1000 genomes]
rs73010402	0.91[ASN][1000 genomes]
rs73876049	0.84[ASN][1000 genomes]
rs73876051	0.84[ASN][1000 genomes]
rs73876052	0.84[ASN][1000 genomes]
rs73876057	0.84[ASN][1000 genomes]
rs73876059	0.84[ASN][1000 genomes]
rs73876061	0.84[ASN][1000 genomes]
rs73876063	0.84[ASN][1000 genomes]
rs73876065	0.82[ASN][1000 genomes]
rs73876066	0.84[ASN][1000 genomes]
rs73876071	0.82[ASN][1000 genomes]
rs73876101	0.91[ASN][1000 genomes]
rs7426713	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7427964	0.85[EUR][1000 genomes]
rs7427978	0.85[EUR][1000 genomes]
rs7429617	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7429718	0.82[AMR][1000 genomes]
rs7431330	0.82[AMR][1000 genomes]
rs7431666	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7433034	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7433394	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7433902	0.85[EUR][1000 genomes]
rs7615986	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7628666	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7630042	0.85[EUR][1000 genomes]
rs7633892	0.91[ASN][1000 genomes]
rs7634217	0.85[EUR][1000 genomes]
rs7640151	0.83[ASN][1000 genomes]
rs7646046	0.85[EUR][1000 genomes]
rs7652225	0.91[ASN][1000 genomes]
rs7652373	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652432	0.85[EUR][1000 genomes]
rs903942	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9810012	0.85[EUR][1000 genomes]
rs9813079	0.83[EUR][1000 genomes]
rs9815680	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9816330	0.82[AMR][1000 genomes]
rs9822252	0.83[CEU][hapmap]
rs9823808	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9831314	0.85[EUR][1000 genomes]
rs9832503	0.85[EUR][1000 genomes]
rs9839765	0.83[CEU][hapmap]
rs9839936	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840341	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9857262	0.81[ASN][1000 genomes]
rs9859293	0.83[CEU][hapmap]
rs9859307	0.85[EUR][1000 genomes]
rs9867696	0.93[ASN][1000 genomes]
rs9870314	0.85[EUR][1000 genomes]
rs9872559	0.93[AFR][1000 genomes]
rs9874108	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9878965	0.84[EUR][1000 genomes]
rs9882410	0.83[EUR][1000 genomes]
rs9882755	0.83[EUR][1000 genomes]
rs9883543	0.93[ASN][1000 genomes]
rs9883974	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006802	chr3:161921063-162599175	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv428424	chr3:162145988-163033943	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1012160	chr3:162182166-162540478	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv592201	chr3:162188625-163142162	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470994	chr3:162217993-162945834	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1005142	chr3:162284967-162447818	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv877758	chr3:162287573-162521339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv877759	chr3:162303276-162521339	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv877761	chr3:162346392-162521339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv592208	chr3:162369863-162437102	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1005637	chr3:162379324-162635451	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv877762	chr3:162400620-162521339	Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv869804	chr3:162414099-162776884	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv829776	chr3:162422424-162577578	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv1001282	chr3:162429561-162513137	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9844124	SCARNA7	cis	cerebellum	SCAN
rs9844124	CD44	trans	lymphoblastoid	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162428400-162431400	Enhancers	Dnd41	blood
2	chr3:162428600-162430600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:162429400-162430000	Enhancers	Colon Smooth Muscle	Colon
4	chr3:162429600-162430000	Enhancers	HSMMtube	muscle

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