Variant report

Variant	rs28661421
Chromosome Location	chr17:38013807-38013808
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 142 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs12709364	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12937330	1.00[EUR][1000 genomes]
rs12938117	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12938617	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12938749	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12940616	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12942660	1.00[EUR][1000 genomes]
rs12945253	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12946040	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12946188	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12946792	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12947480	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12952146	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13313561	1.00[EUR][1000 genomes]
rs13313564	1.00[EUR][1000 genomes]
rs13313573	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13380871	1.00[EUR][1000 genomes]
rs1453560	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1510475	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16965367	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17676923	0.83[EUR][1000 genomes]
rs2313429	1.00[EUR][1000 genomes]
rs28392589	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28403951	1.00[EUR][1000 genomes]
rs28449671	1.00[EUR][1000 genomes]
rs28535471	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28537796	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28580691	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28621669	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28648398	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28651240	0.81[AFR][1000 genomes]
rs28695941	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28723017	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28842324	1.00[EUR][1000 genomes]
rs28880017	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28896477	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2941509	1.00[EUR][1000 genomes]
rs34016964	1.00[EUR][1000 genomes]
rs34053394	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34291217	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34344462	1.00[EUR][1000 genomes]
rs34485135	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34518282	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34582264	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34599546	1.00[EUR][1000 genomes]
rs34640000	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34654193	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34758895	0.92[EUR][1000 genomes]
rs34864615	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs34925681	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34988504	1.00[EUR][1000 genomes]
rs35088469	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35105110	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35130019	0.96[EUR][1000 genomes]
rs35336365	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35352075	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35397078	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35405174	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35506518	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35770042	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35938199	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36097841	1.00[EUR][1000 genomes]
rs4337325	1.00[EUR][1000 genomes]
rs4622539	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56928975	0.96[EUR][1000 genomes]
rs58075375	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66763967	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67135646	1.00[EUR][1000 genomes]
rs67571561	1.00[EUR][1000 genomes]
rs67600807	1.00[EUR][1000 genomes]
rs67605703	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71369788	1.00[EUR][1000 genomes]
rs71369791	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71369792	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7211998	1.00[EUR][1000 genomes]
rs7217133	1.00[EUR][1000 genomes]
rs7224641	1.00[EUR][1000 genomes]
rs73302152	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73304123	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7503018	1.00[EUR][1000 genomes]
rs8067523	1.00[EUR][1000 genomes]
rs8068125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8068894	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8069531	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8069893	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8072612	1.00[EUR][1000 genomes]
rs8076347	1.00[EUR][1000 genomes]
rs8078409	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8079075	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9652838	0.96[EUR][1000 genomes]
rs9652840	1.00[EUR][1000 genomes]
rs9892781	1.00[EUR][1000 genomes]
rs9894370	0.92[EUR][1000 genomes]
rs9894680	1.00[EUR][1000 genomes]
rs9894898	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9896940	0.84[AMR][1000 genomes]
rs9898031	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9898464	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9899006	1.00[EUR][1000 genomes]
rs9899336	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9899345	1.00[EUR][1000 genomes]
rs9900019	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9900538	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9900541	1.00[EUR][1000 genomes]
rs9901483	1.00[EUR][1000 genomes]
rs9901617	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9901917	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9902621	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9904277	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9904834	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9905881	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9907096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9907291	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9907564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9907794	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9907966	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9907988	0.96[EUR][1000 genomes]
rs9908694	1.00[EUR][1000 genomes]
rs9908983	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9909365	1.00[EUR][1000 genomes]
rs9909432	0.89[EUR][1000 genomes]
rs9911069	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9911634	1.00[EUR][1000 genomes]
rs9911669	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9911688	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9912095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9913044	0.96[EUR][1000 genomes]
rs9913596	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9913769	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9913795	1.00[EUR][1000 genomes]
rs9913957	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9914302	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9914516	0.83[EUR][1000 genomes]
rs9914665	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9914757	0.96[EUR][1000 genomes]
rs9915509	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9915797	0.92[EUR][1000 genomes]
rs9916259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9916369	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv1795575	chr17:37974075-38041762	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38000800-38017400	Weak transcription	Thymus	Thymus
2	chr17:38004400-38016800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr17:38005200-38014200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr17:38006200-38017400	Weak transcription	Fetal Thymus	thymus
5	chr17:38007200-38016600	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr17:38009000-38016800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:38009200-38016200	Weak transcription	Primary T cells from cord blood	blood
8	chr17:38012000-38015800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:38012000-38016000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr17:38012800-38014000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr17:38013000-38014000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr17:38013200-38016800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr17:38013400-38014200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr17:38013400-38014600	Enhancers	Primary B cells from cord blood	blood
15	chr17:38013400-38016200	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr17:38013600-38014600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr17:38013800-38015000	Active TSS	GM12878-XiMat	blood
18	chr17:38013800-38015200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr17:38013800-38015400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr17:38013800-38017400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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