Variant report

Variant	rs9621047
Chromosome Location	chr22:31004127-31004128
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	RUNX3	chr22:31003923-31004379	GM12878	blood:	n/a	n/a
2	EBF1	chr22:31003943-31004406	GM12878	blood:	n/a	chr22:31004212-31004223
3	ZNF143	chr22:31004120-31004187	GM12878	blood:	n/a	n/a
4	MTA3	chr22:31003862-31004451	GM12878	blood:	n/a	n/a
5	TCF12	chr22:31004049-31004340	GM12878	blood:	n/a	n/a
6	EGR1	chr22:31003998-31004280	K562	blood:	n/a	chr22:31004143-31004156 chr22:31004143-31004156 chr22:31004144-31004153 chr22:31004159-31004173 chr22:31004143-31004156 chr22:31004142-31004156 chr22:31004144-31004154 chr22:31004138-31004160 chr22:31004144-31004155 chr22:31004140-31004154 chr22:31004143-31004156 chr22:31004144-31004154
7	FOXM1	chr22:31003947-31004415	GM12878	blood:	n/a	n/a
8	EGR1	chr22:31003950-31004276	K562	blood:	n/a	chr22:31004143-31004156 chr22:31004143-31004156 chr22:31004144-31004153 chr22:31004159-31004173 chr22:31004143-31004156 chr22:31004142-31004156 chr22:31004144-31004154 chr22:31004138-31004160 chr22:31004144-31004155 chr22:31004140-31004154 chr22:31004143-31004156 chr22:31004144-31004154
9	EBF1	chr22:31003865-31004370	GM12878	blood:	n/a	chr22:31004212-31004223
10	EBF1	chr22:31003850-31005054	GM12878	blood:	n/a	chr22:31004770-31004780 chr22:31004769-31004782 chr22:31004212-31004223 chr22:31004878-31004887 chr22:31004772-31004781 chr22:31004770-31004783
11	CEBPB	chr22:31003873-31004491	GM12878	blood:	n/a	chr22:31004184-31004195
12	NFIC	chr22:31003988-31004407	GM12878	blood:	n/a	n/a
13	CEBPB	chr22:31004071-31004251	HepG2	liver:	n/a	chr22:31004184-31004195
14	RUNX3	chr22:31004022-31004464	GM12878	blood:	n/a	n/a
15	EGR1	chr22:31003991-31004233	GM12878	blood:	n/a	chr22:31004143-31004156 chr22:31004143-31004156 chr22:31004144-31004153 chr22:31004159-31004173 chr22:31004143-31004156 chr22:31004142-31004156 chr22:31004144-31004154 chr22:31004138-31004160 chr22:31004144-31004155 chr22:31004140-31004154 chr22:31004143-31004156 chr22:31004144-31004154
16	EGR1	chr22:31003974-31004279	GM12878	blood:	n/a	chr22:31004143-31004156 chr22:31004143-31004156 chr22:31004144-31004153 chr22:31004159-31004173 chr22:31004143-31004156 chr22:31004142-31004156 chr22:31004144-31004154 chr22:31004138-31004160 chr22:31004144-31004155 chr22:31004140-31004154 chr22:31004143-31004156 chr22:31004144-31004154

No.	Distal block	Cell Line	Cell type
1	chr22:31001781..31003310-chr22:31003828..31005439,2	K562	blood:
2	chr22:31001608..31004689-chr22:31008894..31012791,3	K562	blood:
3	chr22:30998699..31001313-chr22:31003661..31005659,2	K562	blood:
4	chr22:30986017..30988291-chr22:31003430..31005717,3	K562	blood:

Variant related genes	Relation type
PES1	TF binding region
ENSG00000185339	Chromatin interaction
ENSG00000100029	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11703570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13055009	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13056378	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13057127	0.82[ASN][1000 genomes]
rs1544468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2301955	0.81[ASW][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2301957	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2301958	0.93[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4353747	0.82[ASN][1000 genomes]
rs4820882	0.95[ASN][1000 genomes]
rs4820888	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs4820890	0.89[ASN][1000 genomes]
rs56132790	0.82[ASN][1000 genomes]
rs5749131	0.81[CHB][hapmap]
rs5749132	1.00[ASN][1000 genomes]
rs5749134	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749135	0.81[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749137	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5749142	0.82[ASN][1000 genomes]
rs5749143	0.82[ASN][1000 genomes]
rs5749145	0.82[ASN][1000 genomes]
rs5749148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5753229	0.93[ASN][1000 genomes]
rs5753234	0.99[ASN][1000 genomes]
rs5753246	0.90[ASN][1000 genomes]
rs5753247	0.92[ASN][1000 genomes]
rs5753257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs5753260	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5997703	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5997709	0.81[ASN][1000 genomes]
rs5997710	0.81[ASN][1000 genomes]
rs5997727	0.93[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap]
rs7286680	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7289553	0.82[ASN][1000 genomes]
rs731990	0.82[ASN][1000 genomes]
rs731991	0.82[ASN][1000 genomes]
rs740233	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs740235	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8630	0.93[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap]
rs9609017	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv834175	chr22:30976624-31089545	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9621047	PES1	cis	parietal	SCAN
rs9621047	AP1B1	cis	parietal	SCAN
rs9621047	CRYBB3	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31001400-31006400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr22:31001800-31004400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr22:31002000-31007000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr22:31002200-31004400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr22:31002200-31004800	Weak transcription	Hela-S3	cervix
6	chr22:31002200-31005000	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr22:31002800-31004200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr22:31002800-31004400	Flanking Active TSS	GM12878-XiMat	blood
9	chr22:31003000-31005000	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr22:31003000-31005600	Enhancers	Primary B cells from cord blood	blood
11	chr22:31003200-31004200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:31003200-31004200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr22:31003200-31004200	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr22:31003200-31004200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr22:31003200-31004200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr22:31003200-31004200	Flanking Active TSS	Rectal Smooth Muscle	rectum
17	chr22:31003200-31004400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
18	chr22:31003200-31004400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr22:31003200-31004400	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr22:31003200-31004400	Flanking Active TSS	HUVEC	blood vessel
21	chr22:31003200-31005600	Enhancers	Primary B cells from peripheral blood	blood
22	chr22:31003200-31006000	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr22:31003200-31007000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr22:31003200-31031200	Weak transcription	Aorta	Aorta
25	chr22:31003400-31004200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr22:31003400-31004400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr22:31003400-31004600	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr22:31003400-31005200	Weak transcription	Ovary	ovary
29	chr22:31003400-31005400	Enhancers	Gastric	stomach
30	chr22:31003400-31005800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr22:31003400-31006000	Flanking Active TSS	Colon Smooth Muscle	Colon
32	chr22:31003400-31006400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr22:31003400-31006600	Enhancers	Fetal Thymus	thymus
34	chr22:31003400-31007000	Enhancers	Spleen	Spleen
35	chr22:31003600-31004200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr22:31003600-31004200	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr22:31003600-31004200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr22:31003600-31004200	Enhancers	Liver	Liver
39	chr22:31003600-31004200	Enhancers	Pancreas	Pancrea
40	chr22:31003600-31004600	Weak transcription	HSMMtube	muscle
41	chr22:31003600-31004800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr22:31003600-31004800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr22:31003600-31004800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr22:31003600-31004800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr22:31003600-31004800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr22:31003600-31004800	Enhancers	K562	blood
47	chr22:31003600-31004800	Weak transcription	NH-A	brain
48	chr22:31003600-31004800	Weak transcription	NHEK	skin
49	chr22:31003600-31005000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr22:31003600-31005000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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