Variant report

Variant	rs2267574
Chromosome Location	chr19:35825143-35825144
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:58)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:58 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr19:35825094-35825625	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:35819647-35826483	GM12891	blood:	n/a	n/a
3	IRF4	chr19:35824950-35825457	GM12878	blood:	n/a	n/a
4	RCOR1	chr19:35825034-35825608	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:35824697-35825772	GM12892	blood:	n/a	n/a
6	TBP	chr19:35824914-35825331	GM12878	blood:	n/a	n/a
7	RELA	chr19:35824897-35825588	GM19099	blood:	n/a	n/a
8	POLR2A	chr19:35819682-35826512	GM12878	blood:	n/a	n/a
9	STAT5A	chr19:35824699-35825567	GM12878	blood:	n/a	n/a
10	PML	chr19:35823363-35825812	GM12878	blood:	n/a	n/a
11	PAX5	chr19:35824959-35825709	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:35823459-35826382	GM18505	blood:	n/a	n/a
13	MTA3	chr19:35824520-35825769	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:35823465-35826359	GM19193	blood:	n/a	n/a
15	ZNF143	chr19:35825114-35825200	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:35824715-35825755	GM12891	blood:	n/a	n/a
17	POLR2A	chr19:35819733-35826364	GM12878	blood:	n/a	n/a
18	RUNX3	chr19:35824522-35825770	GM12878	blood:	n/a	n/a
19	STAT1	chr19:35824931-35825306	GM12878	blood:	n/a	n/a
20	PAX5	chr19:35825084-35825324	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:35823509-35825814	GM12891	blood:	n/a	n/a
22	STAT3	chr19:35825109-35825629	GM12878	blood:	n/a	n/a
23	TCF3	chr19:35825091-35825241	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:35823438-35826540	GM12892	blood:	n/a	n/a
25	POLR2A	chr19:35824618-35826326	GM15510	blood:	n/a	n/a
26	RELA	chr19:35824994-35826317	GM15510	blood:	n/a	n/a
27	PBX3	chr19:35825060-35825240	GM12878	blood:	n/a	n/a
28	STAT5A	chr19:35824832-35825756	GM12878	blood:	n/a	n/a
29	TCF12	chr19:35825058-35825315	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:35823503-35826358	GM19099	blood:	n/a	n/a
31	POLR2A	chr19:35819664-35827598	GM12878	blood:	n/a	n/a
32	NFIC	chr19:35824562-35826386	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:35823400-35826525	GM12892	blood:	n/a	n/a
34	ATF2	chr19:35824746-35825679	GM12878	blood:	n/a	n/a
35	BATF	chr19:35825004-35825552	GM12878	blood:	n/a	n/a
36	BCLAF1	chr19:35824765-35825698	GM12878	blood:	n/a	n/a
37	PAX5	chr19:35825046-35825519	GM12892	blood:	n/a	n/a
38	NFATC1	chr19:35824500-35825789	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:35824434-35826488	GM12878	blood:	n/a	n/a
40	RUNX3	chr19:35824882-35825764	GM12878	blood:	n/a	n/a
41	MTA3	chr19:35819478-35825817	GM12878	blood:	n/a	n/a
42	BCL11A	chr19:35824971-35825343	GM12878	blood:	n/a	n/a
43	POU2F2	chr19:35824737-35825257	GM12878	blood:	n/a	n/a
44	BATF	chr19:35825091-35825383	GM12878	blood:	n/a	n/a
45	EP300	chr19:35824875-35825372	GM12878	blood:	n/a	n/a
46	POLR2A	chr19:35824885-35825289	GM12891	blood:	n/a	n/a
47	POLR2A	chr19:35819625-35826402	GM12878	blood:	n/a	n/a
48	WRNIP1	chr19:35822762-35825716	GM12878	blood:	n/a	n/a
49	BHLHE40	chr19:35825068-35826277	GM12878	blood:	n/a	n/a
50	NFIC	chr19:35824957-35825648	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:35824362..35827653-chr19:35833648..35835765,3	K562	blood:
2	chr19:35797829..35800128-chr19:35823862..35825668,2	MCF-7	breast:
3	chr19:35801109..35803995-chr19:35823697..35825261,2	K562	blood:
4	chr19:35808727..35811352-chr19:35824203..35826725,2	MCF-7	breast:

No data

Variant related genes	Relation type
CD22	TF binding region
ENSG00000105695	Chromatin interaction
ENSG00000012124	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10419538	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12185485	0.81[CEU][hapmap]
rs12327820	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs2239512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2267577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv833810	chr19:35782588-35971959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
8	esv1828194	chr19:35812566-35865695	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2267574	ENSG00000012124	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35810400-35835200	Weak transcription	Fetal Lung	lung
2	chr19:35811600-35832200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:35817600-35844000	Weak transcription	Brain Angular Gyrus	brain
4	chr19:35818800-35836600	Weak transcription	Brain Anterior Caudate	brain
5	chr19:35820000-35829000	Strong transcription	Brain Inferior Temporal Lobe	brain
6	chr19:35820400-35827600	Strong transcription	Brain Hippocampus Middle	brain
7	chr19:35820600-35827000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr19:35821000-35825400	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
9	chr19:35822400-35826000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
10	chr19:35823600-35825600	Strong transcription	Brain Cingulate Gyrus	brain
11	chr19:35823600-35825600	Strong transcription	Brain Substantia Nigra	brain
12	chr19:35824200-35837000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:35824400-35825400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr19:35824400-35826800	Weak transcription	Spleen	Spleen
15	chr19:35824400-35828400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:35824600-35825400	Weak transcription	Ovary	ovary
17	chr19:35824600-35828200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr19:35824600-35834400	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr19:35824800-35829400	Genic enhancers	Primary B cells from cord blood	blood
20	chr19:35825000-35825400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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