Variant report

Variant	rs12094548
Chromosome Location	chr1:226116697-226116698
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr1:226115904-226116825	PBDE	blood:	n/a	n/a
2	CBX3	chr1:226115690-226116952	K562	blood:	n/a	n/a
3	ZNF274	chr1:226116061-226116792	K562	blood:	n/a	n/a
4	GATA1	chr1:226115651-226116949	K562	blood:	n/a	n/a
5	MAX	chr1:226115980-226116792	K562	blood:	n/a	n/a
6	TEAD4	chr1:226115648-226116711	K562	blood:	n/a	n/a
7	POLR2A	chr1:226115817-226116712	K562	blood:	n/a	n/a
8	TEAD4	chr1:226115659-226116924	K562	blood:	n/a	n/a
9	TRIM28	chr1:226115640-226116741	K562	blood:	n/a	chr1:226116354-226116362
10	NR2F2	chr1:226114053-226117256	K562	blood:	n/a	n/a
11	EP300	chr1:226115761-226116720	K562	blood:	n/a	chr1:226116506-226116520

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:225963077..225965725-chr1:226115313..226117322,2	K562	blood:
2	chr1:226115016..226118116-chr1:226129058..226132265,3	K562	blood:
3	chr1:226108702..226117785-chr1:226183554..226190529,14	K562	blood:
4	chr1:226069355..226071366-chr1:226115818..226117675,3	K562	blood:
5	chr1:226115314..226117740-chr1:226124602..226127664,3	K562	blood:
6	chr1:225963935..225966560-chr1:226115548..226117659,2	K562	blood:
7	chr1:226069355..226072326-chr1:226116134..226117675,2	K562	blood:
8	chr1:226116139..226117660-chr1:226183554..226185717,2	K562	blood:

No data

Variant related genes	Relation type
PYCR2	TF binding region
ENSG00000255835	TF binding region
ENSG00000143751	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000248322	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000143768	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10915886	0.84[YRI][hapmap]
rs10915887	0.85[YRI][hapmap]
rs10915888	0.84[YRI][hapmap]
rs10915895	0.89[AMR][1000 genomes]
rs10915902	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10915903	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12078868	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080725	0.89[AMR][1000 genomes]
rs12092868	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35273824	0.89[AMR][1000 genomes]
rs35684337	0.89[AMR][1000 genomes]
rs56035614	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6700642	0.81[AMR][1000 genomes]
rs74150558	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150559	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150561	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv3335650	chr1:226074720-226125458	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv3369235	chr1:226075748-226127738	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv468216	chr1:226078915-226135132	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv549267	chr1:226078915-226135132	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv535314	chr1:226087226-226128261	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12094548	PYCR2	cis	multi-tissue	Pritchard

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226112600-226117400	Enhancers	Primary T cells from cord blood	blood
2	chr1:226112600-226125200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:226112600-226126800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:226112600-226126800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:226112800-226120800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:226112800-226126800	Weak transcription	Right Atrium	heart
7	chr1:226113000-226124000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:226113000-226124400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:226113800-226118200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr1:226114000-226116800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr1:226114200-226117200	Enhancers	Fetal Thymus	thymus
12	chr1:226114200-226117400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:226114600-226120600	Weak transcription	Osteobl	bone
14	chr1:226114800-226118800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:226114800-226127000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:226115600-226116800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:226115600-226116800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:226115600-226117000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr1:226115600-226117000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr1:226115600-226117000	Flanking Active TSS	K562	blood
21	chr1:226115600-226117400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:226115600-226117400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr1:226115600-226117400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:226115800-226117400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:226116000-226117800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:226116200-226116800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:226116200-226117400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:226116200-226118600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:226116400-226117000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:226116400-226124600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:226116600-226126800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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