Variant report

Variant	rs13053923
Chromosome Location	chr22:30988382-30988383
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	TCF12	chr22:30987638-30988460	ECC-1	luminal epithelium:	n/a	n/a
2	GATA2	chr22:30988012-30988425	SH-SY5Y	brain:	n/a	chr22:30988393-30988404 chr22:30988108-30988121
3	FOXM1	chr22:30987830-30988584	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr22:30988026-30988388	HUVEC	blood vessel:	n/a	n/a
5	SP4	chr22:30987636-30988386	H1-hESC	embryonic stem cell:	n/a	chr22:30988167-30988178
6	ZNF143	chr22:30987697-30988457	GM12878	blood:	n/a	n/a
7	YY1	chr22:30987746-30988509	SK-N-SH_RA	brain:	n/a	n/a
8	MYC	chr22:30987108-30988538	A549	lung:	n/a	n/a
9	PAX5	chr22:30987922-30988450	GM12878	blood:	n/a	n/a
10	MAX	chr22:30987699-30988417	GM12878	blood:	n/a	n/a
11	NRF1	chr22:30988077-30988406	Hela-S3	cervix:	n/a	n/a
12	SP1	chr22:30987629-30988480	A549	lung:	n/a	chr22:30987757-30987767 chr22:30988316-30988325 chr22:30988167-30988178
13	RELA	chr22:30987757-30988409	GM19099	blood:	n/a	chr22:30987977-30987986 chr22:30987977-30987986
14	PML	chr22:30987138-30988569	GM12878	blood:	n/a	n/a
15	SP1	chr22:30987761-30988423	H1-hESC	embryonic stem cell:	n/a	chr22:30988316-30988325 chr22:30988167-30988178
16	USF1	chr22:30987668-30988395	SK-N-SH	brain:	n/a	chr22:30987878-30987887
17	SP1	chr22:30987748-30988497	A549	lung:	n/a	chr22:30987757-30987767 chr22:30988316-30988325 chr22:30988167-30988178
18	USF1	chr22:30987600-30988439	ECC-1	luminal epithelium:	n/a	chr22:30987878-30987887
19	SPI1	chr22:30987631-30988539	HL-60	blood:	n/a	n/a
20	MAZ	chr22:30987750-30988388	HepG2	liver:	n/a	n/a
21	CHD2	chr22:30987758-30988420	GM12878	blood:	n/a	n/a
22	SIX5	chr22:30987714-30988399	A549	lung:	n/a	n/a
23	TCF12	chr22:30987695-30988534	ECC-1	luminal epithelium:	n/a	n/a
24	CREB1	chr22:30987670-30988411	HepG2	liver:	n/a	n/a
25	GABPA	chr22:30987666-30988430	MCF-7	breast:	n/a	n/a
26	ELF1	chr22:30987766-30988482	A549	lung:	n/a	n/a
27	ATF3	chr22:30987991-30988424	K562	blood:	n/a	n/a
28	MAZ	chr22:30986755-30988532	IMR90	lung:	n/a	n/a
29	ZBTB7A	chr22:30988198-30988391	K562	blood:	n/a	n/a
30	REST	chr22:30987413-30988751	H1-neurons	neurons:	n/a	chr22:30988185-30988198
31	HCFC1	chr22:30986827-30988481	Hela-S3	cervix:	n/a	n/a
32	SIN3A	chr22:30987163-30988473	H1-hESC	embryonic stem cell:	n/a	n/a
33	YY1	chr22:30988009-30988430	GM12878	blood:	n/a	n/a
34	SIX5	chr22:30987832-30988407	H1-hESC	embryonic stem cell:	n/a	n/a
35	TBP	chr22:30987282-30988386	K562	blood:	n/a	n/a
36	BHLHE40	chr22:30987244-30988382	HepG2	liver:	n/a	chr22:30987878-30987887
37	ZMIZ1	chr22:30987794-30988389	K562	blood:	n/a	n/a
38	GABPA	chr22:30987717-30988383	A549	lung:	n/a	n/a
39	TBP	chr22:30987630-30988458	H1-hESC	embryonic stem cell:	n/a	n/a
40	ELF1	chr22:30987591-30988427	GM12878	blood:	n/a	chr22:30987744-30987756
41	ATF3	chr22:30987950-30988424	A549	lung:	n/a	n/a
42	YY1	chr22:30988081-30988383	K562	blood:	n/a	n/a
43	CREB1	chr22:30987642-30988536	K562	blood:	n/a	n/a
44	POLR2A	chr22:30987664-30988559	H1-neurons	neurons:	n/a	n/a
45	MYC	chr22:30987341-30988441	NB4	blood:	n/a	n/a
46	ETS1	chr22:30987669-30988382	GM12878	blood:	n/a	n/a
47	CHD2	chr22:30987675-30988416	H1-hESC	embryonic stem cell:	n/a	n/a
48	SIX5	chr22:30987947-30988414	K562	blood:	n/a	n/a
49	BCLAF1	chr22:30987794-30988471	K562	blood:	n/a	chr22:30988287-30988300
50	RCOR1	chr22:30987798-30988438	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:30987737..30989936-chr22:31002004..31003702,2	MCF-7	breast:

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

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11089465	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2072198	0.88[ASN][1000 genomes]
rs35062974	0.83[ASN][1000 genomes]
rs4820871	0.84[ASN][1000 genomes]
rs4820872	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4820875	0.89[ASN][1000 genomes]
rs4820876	1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4820878	0.92[ASN][1000 genomes]
rs5749131	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs5997692	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5997694	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs5997697	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62227016	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs737953	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv588887	chr22:30953521-30995356	Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	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
rs13053923	TCN2	cis	multi-tissue	Pritchard
rs13053923	LOC730005	cis	brain	BrainEAC
rs13053923	CRYBB3	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30986400-30988600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr22:30986600-30988600	Active TSS	Fetal Kidney	kidney
3	chr22:30986800-30988400	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr22:30986800-30988600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr22:30986800-30988600	Active TSS	Psoas Muscle	Psoas
6	chr22:30986800-30988600	Active TSS	A549	lung
7	chr22:30987000-30988400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr22:30987000-30988400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr22:30987000-30988400	Active TSS	Left Ventricle	heart
10	chr22:30987000-30988600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr22:30987000-30988600	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr22:30987000-30988600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr22:30987000-30988600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr22:30987000-30988600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr22:30987000-30988600	Active TSS	HSMM	muscle
16	chr22:30987000-30988600	Active TSS	NHDF-Ad	bronchial
17	chr22:30987000-30988600	Active TSS	NHEK	skin
18	chr22:30987200-30988400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr22:30987200-30988400	Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr22:30987200-30988400	Active TSS	Muscle Satellite Cultured Cells	--
21	chr22:30987200-30988400	Active TSS	Fetal Stomach	stomach
22	chr22:30987200-30988400	Active TSS	Hela-S3	cervix
23	chr22:30987200-30988400	Active TSS	NHLF	lung
24	chr22:30987200-30988400	Active TSS	Osteobl	bone
25	chr22:30987200-30988600	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr22:30987200-30988600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr22:30987200-30988600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr22:30987200-30988600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr22:30987200-30988600	Active TSS	Ovary	ovary
30	chr22:30987200-30988600	Active TSS	HSMMtube	muscle
31	chr22:30987400-30988400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr22:30987400-30988400	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr22:30987400-30988400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr22:30987400-30988400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr22:30987400-30988400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr22:30987400-30988400	Active TSS	Brain Germinal Matrix	brain
37	chr22:30987400-30988400	Active TSS	Brain Hippocampus Middle	brain
38	chr22:30987400-30988400	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr22:30987400-30988400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr22:30987400-30988400	Active TSS	Esophagus	oesophagus
41	chr22:30987400-30988400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr22:30987400-30988400	Active TSS	Fetal Lung	lung
43	chr22:30987400-30988400	Active TSS	Pancreas	Pancrea
44	chr22:30987400-30988400	Active TSS	Rectal Smooth Muscle	rectum
45	chr22:30987400-30988400	Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr22:30987400-30988600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr22:30987400-30988600	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr22:30987400-30988600	Active TSS	Brain Anterior Caudate	brain
49	chr22:30987400-30988600	Active TSS	Brain Cingulate Gyrus	brain
50	chr22:30987400-30988600	Active TSS	Brain Substantia Nigra	brain

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