Variant report

Variant	rs3123641
Chromosome Location	chr1:174611708-174611709
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10489262	1.00[EUR][1000 genomes]
rs10912792	0.86[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10912794	1.00[EUR][1000 genomes]
rs10912801	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10912808	1.00[EUR][1000 genomes]
rs10912809	1.00[EUR][1000 genomes]
rs10912815	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912816	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912818	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912819	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912847	1.00[EUR][1000 genomes]
rs12057161	1.00[EUR][1000 genomes]
rs12057359	0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12059051	0.86[LWK][hapmap];1.00[TSI][hapmap]
rs12064144	1.00[EUR][1000 genomes]
rs12066268	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12066421	1.00[EUR][1000 genomes]
rs12066736	1.00[EUR][1000 genomes]
rs12067772	1.00[EUR][1000 genomes]
rs12067791	1.00[EUR][1000 genomes]
rs12069689	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12070505	1.00[EUR][1000 genomes]
rs12072909	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12075213	0.86[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12077283	1.00[EUR][1000 genomes]
rs12077880	1.00[EUR][1000 genomes]
rs12078714	1.00[EUR][1000 genomes]
rs12080070	1.00[EUR][1000 genomes]
rs12080242	1.00[EUR][1000 genomes]
rs12088650	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12092811	0.86[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12094140	0.83[LWK][hapmap];1.00[TSI][hapmap]
rs12096717	1.00[EUR][1000 genomes]
rs1231828	1.00[EUR][1000 genomes]
rs12354111	1.00[EUR][1000 genomes]
rs1329280	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1612104	0.93[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1618234	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1653631	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1653633	1.00[EUR][1000 genomes]
rs1653637	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847096	1.00[EUR][1000 genomes]
rs16847457	1.00[EUR][1000 genomes]
rs173000	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1754356	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17838246	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs189141	0.83[ASW][hapmap];0.88[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2116515	1.00[EUR][1000 genomes]
rs2760059	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2981891	1.00[EUR][1000 genomes]
rs2981895	1.00[EUR][1000 genomes]
rs2987871	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2987878	1.00[EUR][1000 genomes]
rs3018408	0.84[AMR][1000 genomes]
rs332766	0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs332775	1.00[EUR][1000 genomes]
rs332780	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs332785	0.83[ASW][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs332790	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs332792	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs333419	0.83[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs333425	1.00[EUR][1000 genomes]
rs333434	1.00[EUR][1000 genomes]
rs35582650	1.00[EUR][1000 genomes]
rs392368	0.94[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4290116	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4309037	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs454643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55659406	1.00[EUR][1000 genomes]
rs56106555	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56357087	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58238388	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59073370	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60283543	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6672781	1.00[EUR][1000 genomes]
rs6696432	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6701696	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74126848	1.00[EUR][1000 genomes]
rs74126851	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74126855	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7525430	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv534381	chr1:174468168-174656796	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv1803591	chr1:174594575-174642336	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174603200-174616000	Weak transcription	Fetal Intestine Large	intestine
2	chr1:174604600-174613800	Weak transcription	Ovary	ovary
3	chr1:174605400-174612400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:174606200-174621600	Weak transcription	Fetal Intestine Small	intestine
5	chr1:174607000-174612000	Weak transcription	Aorta	Aorta
6	chr1:174607000-174612000	Weak transcription	Left Ventricle	heart
7	chr1:174607000-174618200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:174607400-174613200	Weak transcription	Primary T cells from cord blood	blood
9	chr1:174607400-174613400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:174607600-174613000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:174607600-174613200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:174607600-174628600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:174607600-174637000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr1:174607600-174677800	Weak transcription	Primary B cells from cord blood	blood
15	chr1:174611600-174612000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:174611600-174612000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood

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