Variant report

Variant	rs2607258
Chromosome Location	chr19:51972427-51972428
allele	A/G
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	POLR2A	chr19:51971107-51973140	K562	blood:	n/a	n/a
2	POLR2A	chr19:51970702-51973376	K562	blood:	n/a	n/a
3	MAX	chr19:51972333-51972868	K562	blood:	n/a	chr19:51972711-51972720
4	HEY1	chr19:51971106-51972839	K562	blood:	n/a	n/a
5	POLR2A	chr19:51970738-51973354	K562	blood:	n/a	n/a
6	POLR2A	chr19:51971132-51973240	K562	blood:	n/a	n/a
7	TBP	chr19:51972065-51972760	K562	blood:	n/a	n/a
8	UBTF	chr19:51971094-51973051	K562	blood:	n/a	n/a
9	MYC	chr19:51971178-51973064	K562	blood:	n/a	chr19:51972711-51972720
10	TBL1XR1	chr19:51970726-51973188	K562	blood:	n/a	n/a
11	ZC3H11A	chr19:51972234-51972647	K562	blood:	n/a	n/a
12	MAX	chr19:51972199-51972965	K562	blood:	n/a	chr19:51972711-51972720
13	EP300	chr19:51969868-51973060	K562	blood:	n/a	n/a
14	RCOR1	chr19:51971137-51973169	K562	blood:	n/a	n/a
15	ZNF143	chr19:51971861-51972523	K562	blood:	n/a	chr19:51972044-51972062 chr19:51972400-51972419 chr19:51972317-51972332
16	POLR2A	chr19:51971124-51973390	K562	blood:	n/a	n/a
17	ARID3A	chr19:51972311-51972737	K562	blood:	n/a	n/a
18	ZBTB7A	chr19:51972409-51972680	K562	blood:	n/a	n/a
19	MYC	chr19:51971214-51973105	K562	blood:	n/a	chr19:51972711-51972720
20	POLR2A	chr19:51971138-51973221	K562	blood:	n/a	n/a
21	IRF1	chr19:51969267-51973066	K562	blood:	n/a	chr19:51972064-51972078 chr19:51971883-51971892 chr19:51971396-51971405
22	SIN3AK20	chr19:51972414-51972835	K562	blood:	n/a	n/a
23	IRF1	chr19:51970753-51973090	K562	blood:	n/a	chr19:51972064-51972078 chr19:51971883-51971892 chr19:51971396-51971405
24	POLR2A	chr19:51971152-51973062	K562	blood:	n/a	n/a
25	MAZ	chr19:51971134-51972759	K562	blood:	n/a	chr19:51972711-51972720
26	MAX	chr19:51972249-51973069	K562	blood:	n/a	chr19:51972711-51972720
27	MAX	chr19:51971267-51972906	NB4	blood:	n/a	chr19:51972711-51972720
28	JUN	chr19:51972088-51972680	K562	blood:	n/a	n/a
29	POLR2A	chr19:51971580-51973267	K562	blood:	n/a	n/a
30	TEAD4	chr19:51970779-51973013	K562	blood:	n/a	n/a
31	MYC	chr19:51971216-51972932	K562	blood:	n/a	chr19:51972711-51972720
32	HMGN3	chr19:51972300-51972478	K562	blood:	n/a	n/a
33	JUND	chr19:51970783-51972768	K562	blood:	n/a	chr19:51971884-51971892
34	POLR2A	chr19:51971104-51972639	K562	blood:	n/a	n/a
35	POLR2A	chr19:51971096-51973184	K562	blood:	n/a	n/a
36	E2F6	chr19:51972382-51972821	K562	blood:	n/a	n/a
37	POLR2A	chr19:51972255-51973359	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51970891..51972816-chr19:51977892..51980633,2	K562	blood:
2	chr19:51943317..51945909-chr19:51971726..51974362,2	K562	blood:
3	chr19:51971316..51973681-chr19:51979133..51981319,3	K562	blood:

Variant related genes	Relation type
SIGLEC26P	TF binding region
ENSG00000213822	Chromatin interaction
ENSG00000269181	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10424482	0.87[EUR][1000 genomes]
rs10424572	0.98[EUR][1000 genomes]
rs10424783	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10424804	1.00[CEU][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs11878257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878282	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878388	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11881105	0.94[EUR][1000 genomes]
rs16982729	1.00[CEU][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17206902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs185254	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2607257	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607259	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2607260	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28539101	1.00[EUR][1000 genomes]
rs28607420	0.87[EUR][1000 genomes]
rs2864090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864091	1.00[EUR][1000 genomes]
rs2864092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864093	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs36502	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs36503	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56799568	0.98[EUR][1000 genomes]
rs61201251	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62115066	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62116369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62116370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62116371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62116417	0.98[EUR][1000 genomes]
rs62116418	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62116419	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62116420	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62116422	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7246811	0.98[EUR][1000 genomes]
rs8101777	1.00[CEU][hapmap];0.92[GIH][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs8107537	0.98[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	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv458724	chr19:51925519-51975723	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv579965	chr19:51925519-51975723	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv961163	chr19:51971394-51976393	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2607258	ZNF460	cis	parietal	SCAN
rs2607258	ZNF480	cis	cerebellum	SCAN
rs2607258	SIGLEC12	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51964600-51973000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:51966800-51973400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr19:51969000-51972600	Enhancers	Primary hematopoietic stem cells	blood
4	chr19:51971800-51973000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:51971800-51974200	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr19:51971800-51975000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr19:51972000-51976000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr19:51972200-51973400	Flanking Active TSS	K562	blood

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