Variant report

Variant	rs4871481
Chromosome Location	chr8:125269286-125269287
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	SPI1	chr8:125269005-125269522	HL-60	blood:	n/a	chr8:125269183-125269196
2	SPI1	chr8:125269068-125269392	GM12891	blood:	n/a	chr8:125269183-125269196
3	SPI1	chr8:125268830-125269551	GM12878	blood:	n/a	chr8:125269183-125269196
4	MXI1	chr8:125269239-125269332	GM12878	blood:	n/a	n/a
5	SPI1	chr8:125269151-125269351	GM12878	blood:	n/a	chr8:125269183-125269196
6	SPI1	chr8:125269048-125269392	GM12878	blood:	n/a	chr8:125269183-125269196
7	SPI1	chr8:125269076-125269453	GM12891	blood:	n/a	chr8:125269183-125269196

No.	Distal block	Cell Line	Cell type
1	chr8:125261519..125263579-chr8:125267585..125270166,2	K562	blood:
2	chr8:125265421..125269715-chr8:125283208..125285335,3	MCF-7	breast:
3	chr8:125266902..125269878-chr8:125272603..125275281,2	MCF-7	breast:
4	chr8:125262127..125264204-chr8:125266153..125270131,3	MCF-7	breast:

Variant related genes	Relation type
RNU6-756P	TF binding region
ENSG00000206724	Chromatin interaction
ENSG00000253227	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10087001	0.82[ASN][1000 genomes]
rs10087062	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10087137	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10087222	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10087374	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10091808	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10092616	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13439237	1.00[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13439439	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13439443	0.81[CHB][hapmap]
rs16899475	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs17295226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17295548	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17360690	0.85[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs17360711	0.85[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs17360746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17360788	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4360277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs4374970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4504618	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4593526	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4871476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4871477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4871478	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4871480	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55784871	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55945711	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56068026	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56383080	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60167901	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60995425	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66467223	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66961607	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67153514	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67712436	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67815046	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68047305	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6984141	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6984458	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6984642	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6984921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6986310	0.89[EUR][1000 genomes]
rs7003974	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7011052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7011213	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7011528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72719397	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73345110	0.82[ASN][1000 genomes]
rs73345113	0.82[ASN][1000 genomes]
rs73345158	0.82[ASN][1000 genomes]
rs7842882	0.92[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9297691	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs9297693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9643192	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9969472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9969473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9969475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9969479	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9969480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9969624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762769	chr8:125167256-125480574	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4871481	RP11-383J24.1	cis	Muscle Skeletal	GTEx
rs4871481	TRMT12	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125258400-125282800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr8:125259600-125273800	Weak transcription	Left Ventricle	heart
3	chr8:125260000-125269400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr8:125263600-125270800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr8:125264200-125272600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr8:125264200-125273000	Weak transcription	Primary T cells from cord blood	blood
7	chr8:125264400-125272200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr8:125264400-125272600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr8:125266200-125269800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr8:125266200-125270000	Enhancers	Primary B cells from cord blood	blood
11	chr8:125266200-125271000	Enhancers	Primary B cells from peripheral blood	blood
12	chr8:125267000-125269800	Enhancers	GM12878-XiMat	blood
13	chr8:125267200-125269800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr8:125267600-125269400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr8:125268000-125270000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr8:125268000-125273400	Weak transcription	Fetal Intestine Large	intestine
17	chr8:125268200-125271200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr8:125268200-125272200	Weak transcription	Hela-S3	cervix
19	chr8:125268200-125273400	Weak transcription	A549	lung
20	chr8:125268400-125269400	Weak transcription	Gastric	stomach
21	chr8:125268400-125270200	Weak transcription	Pancreas	Pancrea
22	chr8:125268400-125273600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr8:125268400-125273800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr8:125268400-125273800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr8:125268600-125269400	Enhancers	Placenta	Placenta
26	chr8:125268600-125273400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr8:125268600-125273400	Weak transcription	HUVEC	blood vessel
28	chr8:125268800-125269400	Enhancers	Fetal Brain Male	brain
29	chr8:125268800-125273400	Weak transcription	Fetal Intestine Small	intestine
30	chr8:125268800-125273800	Weak transcription	Spleen	Spleen
31	chr8:125269000-125270800	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr8:125269000-125273800	Weak transcription	Rectal Mucosa Donor 29	rectum

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