Variant report

Variant	rs12092868
Chromosome Location	chr1:226115050-226115051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr1:226114127-226115460	K562	blood:	n/a	chr1:226114399-226114410
2	TEAD4	chr1:226115026-226115453	K562	blood:	n/a	n/a
3	GATA2	chr1:226114981-226115413	K562	blood:	n/a	n/a
4	GATA1	chr1:226114917-226115464	PBDE	blood:	n/a	n/a
5	NR2F2	chr1:226114053-226117256	K562	blood:	n/a	n/a
6	RCOR1	chr1:226114666-226115156	K562	blood:	n/a	n/a
7	ELF1	chr1:226114393-226115063	K562	blood:	n/a	chr1:226114946-226114955 chr1:226114945-226114954

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:226025653..226027789-chr1:226114675..226116510,2	K562	blood:
2	chr1:226115016..226118116-chr1:226129058..226132265,3	K562	blood:
3	chr1:226108702..226117785-chr1:226183554..226190529,14	K562	blood:
4	chr1:226110464..226115809-chr1:226185735..226190763,7	K562	blood:
5	chr1:226113187..226115490-chr1:226126660..226128244,2	K562	blood:
6	chr1:226067470..226074101-chr1:226108823..226116408,13	MCF-7	breast:
7	chr1:226085907..226088745-chr1:226113166..226115980,2	K562	blood:
8	chr1:226070971..226073106-chr1:226113461..226115401,2	MCF-7	breast:

No data

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

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10915895	0.89[AMR][1000 genomes]
rs10915902	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10915903	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12078868	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080725	0.89[AMR][1000 genomes]
rs12094548	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35273824	0.89[AMR][1000 genomes]
rs35684337	0.89[AMR][1000 genomes]
rs56035614	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6700642	0.81[AMR][1000 genomes]
rs74150558	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150559	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74150561	0.82[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

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226112000-226115800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:226112600-226117400	Enhancers	Primary T cells from cord blood	blood
3	chr1:226112600-226125200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:226112600-226126800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:226112600-226126800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:226112800-226115800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:226112800-226120800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:226112800-226126800	Weak transcription	Right Atrium	heart
9	chr1:226113000-226116200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:226113000-226116400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:226113000-226124000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:226113000-226124400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:226113200-226116000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:226113200-226116200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:226113800-226115800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:226113800-226118200	Enhancers	Primary T cells fromperipheralblood	blood
17	chr1:226114000-226115200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr1:226114000-226116200	Enhancers	Primary hematopoietic stem cells	blood
19	chr1:226114000-226116800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr1:226114200-226115200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr1:226114200-226115200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:226114200-226115200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr1:226114200-226115200	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr1:226114200-226117200	Enhancers	Fetal Thymus	thymus
25	chr1:226114200-226117400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:226114600-226115800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:226114600-226120600	Weak transcription	Osteobl	bone
28	chr1:226114800-226115200	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr1:226114800-226115200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:226114800-226116000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:226114800-226116000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:226114800-226118800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:226114800-226127000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:226115000-226115600	Enhancers	K562	blood

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