Variant report

Variant	rs12946040
Chromosome Location	chr17:38000018-38000019
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr17:37999188-38000123	GM12878	blood:	n/a	n/a
2	BATF	chr17:37999747-38000074	GM12878	blood:	n/a	n/a
3	EBF1	chr17:37999844-38000047	GM12878	blood:	n/a	n/a
4	POLR2A	chr17:37999050-38000115	GM12878	blood:	n/a	n/a
5	RUNX3	chr17:37999583-38000143	GM12878	blood:	n/a	n/a
6	NFIC	chr17:37999163-38000191	GM12878	blood:	n/a	n/a
7	MEF2C	chr17:37999526-38000198	GM12878	blood:	n/a	chr17:37999624-37999641 chr17:37999626-37999641 chr17:37999882-37999903 chr17:37999882-37999903 chr17:37999885-37999900
8	NFIC	chr17:37999421-38000108	GM12878	blood:	n/a	n/a
9	POLR2A	chr17:37999009-38000069	GM12891	blood:	n/a	n/a
10	MEF2A	chr17:37999580-38000138	GM12878	blood:	n/a	chr17:37999624-37999641 chr17:37999626-37999641 chr17:37999882-37999903 chr17:37999882-37999903
11	ZNF384	chr17:37999560-38000251	GM12878	blood:	n/a	n/a
12	EBF1	chr17:37999855-38000143	GM12878	blood:	n/a	n/a
13	MTA3	chr17:37999032-38000206	GM12878	blood:	n/a	n/a
14	MEF2A	chr17:37999493-38000181	GM12878	blood:	n/a	chr17:37999624-37999641 chr17:37999626-37999641 chr17:37999882-37999903 chr17:37999882-37999903
15	POLR2A	chr17:37999666-38000088	GM12878	blood:	n/a	n/a
16	BCLAF1	chr17:37999571-38000078	GM12878	blood:	n/a	n/a
17	ATF2	chr17:37999211-38000194	GM12878	blood:	n/a	n/a
18	BCLAF1	chr17:37999056-38000188	GM12878	blood:	n/a	n/a
19	POLR2A	chr17:37999110-38000728	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:37993320..37996437-chr17:37998688..38001239,3	K562	blood:
2	chr17:37997862..38000754-chr17:38065312..38067694,2	K562	blood:

Variant related genes	Relation type
ENSG00000226117	TF binding region
ENSG00000226117	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs12709364	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12937330	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12938117	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12938617	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12938749	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12940616	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12942660	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12945253	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12946188	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12946792	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12947480	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12948686	0.81[AFR][1000 genomes]
rs12952146	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13313561	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13313564	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13313573	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13380871	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1453560	0.96[EUR][1000 genomes]
rs1510475	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16965367	1.00[EUR][1000 genomes]
rs17676923	0.83[EUR][1000 genomes]
rs2313429	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28392589	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28403951	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28449671	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28535471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28537796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28580691	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28621669	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28648398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28661421	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28695941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28723017	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28842324	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28880017	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28896477	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2941509	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34016964	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34053394	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34291217	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34344462	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34485135	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34518282	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34582264	0.88[EUR][1000 genomes]
rs34599546	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34640000	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34654193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34758895	0.92[EUR][1000 genomes]
rs34864615	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34925681	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34988504	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35088469	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35105110	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35130019	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35336365	0.86[EUR][1000 genomes]
rs35352075	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35397078	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35405174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35506518	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35770042	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35938199	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36097841	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4337325	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4622539	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56928975	0.96[EUR][1000 genomes]
rs58075375	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66763967	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67135646	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67571561	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67600807	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67605703	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71369788	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71369791	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71369792	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7211998	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7217133	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7224641	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73302152	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73304123	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7503018	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8067523	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8068125	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8068894	1.00[EUR][1000 genomes]
rs8069531	1.00[EUR][1000 genomes]
rs8069893	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8072612	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8076347	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8078409	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs8079075	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9652838	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9652840	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9892781	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9894370	0.92[EUR][1000 genomes]
rs9894680	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9894898	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9896940	0.84[AMR][1000 genomes]
rs9898031	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9898464	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9899006	1.00[EUR][1000 genomes]
rs9899336	1.00[EUR][1000 genomes]
rs9899345	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9900019	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9900538	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9900541	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9901483	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9901617	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9901917	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9902621	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9904277	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9904834	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9905881	1.00[EUR][1000 genomes]
rs9907096	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9907291	1.00[EUR][1000 genomes]
rs9907564	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9907794	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9907966	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9907988	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9908694	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9908983	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9909365	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9909432	0.89[EUR][1000 genomes]
rs9911069	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9911634	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9911669	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9911688	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9912095	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9913044	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9913596	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9913769	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9913795	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9913957	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9914302	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9914516	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9914665	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9914757	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9915509	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9915797	0.92[EUR][1000 genomes]
rs9916259	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][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	chr17:37996400-38001400	Genic enhancers	Primary B cells from peripheral blood	blood
2	chr17:37996400-38001400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr17:37997400-38005000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr17:37997800-38001400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:37998600-38000800	Enhancers	Thymus	Thymus
6	chr17:37998600-38001000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:37998600-38001000	Enhancers	Fetal Thymus	thymus
8	chr17:37999200-38000400	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr17:37999200-38000600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr17:37999400-38000200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr17:37999600-38000200	Active TSS	GM12878-XiMat	blood
12	chr17:37999600-38000800	Enhancers	Primary B cells from cord blood	blood
13	chr17:37999600-38006200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr17:37999800-38000200	Enhancers	Primary T cells fromperipheralblood	blood
15	chr17:37999800-38000200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr17:37999800-38000800	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr17:37999800-38002600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr17:37999800-38003400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr17:38000000-38005000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr17:38000000-38006000	Enhancers	Primary T helper cells fromperipheralblood	blood

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