Variant report

Variant	rs13056977
Chromosome Location	chr22:29710360-29710361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr22:29710138-29710976	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr22:29710241-29711608	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr22:29710163-29710557	MCF10A-Er-Src	breast:	n/a	n/a
4	CTCF	chr22:29710340-29710630	SAEC	small airway:	n/a	n/a
5	POLR2A	chr22:29710206-29710442	MCF-7	breast:	n/a	n/a
6	NFIC	chr22:29710166-29710597	ECC-1	luminal epithelium:	n/a	chr22:29710313-29710330

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29709318..29711551-chr22:29712533..29715035,2	K562	blood:
2	chr22:29706961..29711668-chr22:29712911..29717067,5	MCF-7	breast:
3	chr22:29710051..29711801-chr22:29712827..29715035,2	K562	blood:
4	chr22:29689537..29691644-chr22:29709816..29711551,2	MCF-7	breast:
5	chr22:29704698..29709036-chr22:29709270..29712865,10	MCF-7	breast:
6	chr22:29700857..29704420-chr22:29708764..29712339,6	MCF-7	breast:

No data

Variant related genes	Relation type
RASL10A	TF binding region
ENSG00000182944	Chromatin interaction
ENSG00000273216	Chromatin interaction
ENSG00000100276	Chromatin interaction
ENSG00000185340	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2301587	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5752899	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5752900	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5752902	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5763131	1.00[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5763140	1.00[ASW][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs5763180	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5763181	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73156524	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv829154	chr22:29617485-29724001	Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv829155	chr22:29664396-29724001	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS 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 target site	21 gene(s)	inside rSNPs	diseases
5	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv914959	chr22:29696438-29712874	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv914960	chr22:29696438-29714069	Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13056977	PIWIL3	cis	cerebellum	SCAN
rs13056977	ASCC2	cis	parietal	SCAN
rs13056977	TPST2	cis	cerebellum	SCAN
rs13056977	CABIN1	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29706600-29711000	Bivalent Enhancer	Fetal Stomach	stomach
2	chr22:29707400-29710400	Weak transcription	K562	blood
3	chr22:29707400-29740000	Weak transcription	Hela-S3	cervix
4	chr22:29708000-29710400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr22:29708400-29711400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
6	chr22:29708600-29711000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
7	chr22:29708600-29711200	Enhancers	Lung	lung
8	chr22:29708800-29710600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
9	chr22:29708800-29710800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
10	chr22:29708800-29710800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr22:29708800-29712200	Bivalent/Poised TSS	Fetal Brain Female	brain
12	chr22:29709000-29710600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr22:29709000-29710800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr22:29709000-29710800	Enhancers	Left Ventricle	heart
15	chr22:29709000-29710800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
16	chr22:29709000-29711000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr22:29709000-29711000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
18	chr22:29709000-29711000	Bivalent Enhancer	Fetal Intestine Large	intestine
19	chr22:29709000-29711000	Bivalent Enhancer	Fetal Intestine Small	intestine
20	chr22:29709000-29711200	Bivalent Enhancer	Stomach Mucosa	stomach
21	chr22:29709200-29710400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr22:29709200-29710400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
23	chr22:29709200-29710600	Bivalent Enhancer	Primary B cells from cord blood	blood
24	chr22:29709200-29711000	Enhancers	Pancreas	Pancrea
25	chr22:29709200-29711000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
26	chr22:29709200-29711200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
27	chr22:29709200-29711400	Enhancers	Gastric	stomach
28	chr22:29709200-29711400	Bivalent Enhancer	Small Intestine	intestine
29	chr22:29709200-29711800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
30	chr22:29709400-29711000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr22:29709400-29711000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr22:29709400-29711000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr22:29709400-29711200	Bivalent Enhancer	Fetal Heart	heart
34	chr22:29709600-29710400	Flanking Bivalent TSS/Enh	Rectal Smooth Muscle	rectum
35	chr22:29709600-29710400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
36	chr22:29709600-29710600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr22:29709600-29710600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr22:29709600-29710600	Bivalent Enhancer	Esophagus	oesophagus
39	chr22:29709600-29710600	Bivalent Enhancer	Spleen	Spleen
40	chr22:29709600-29710800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
41	chr22:29709600-29711000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
42	chr22:29709600-29711000	Bivalent Enhancer	Brain Germinal Matrix	brain
43	chr22:29709600-29711200	Bivalent Enhancer	Placenta	Placenta
44	chr22:29709800-29710400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
45	chr22:29709800-29710400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
46	chr22:29709800-29710400	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr22:29709800-29710600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr22:29709800-29710600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
49	chr22:29709800-29710600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
50	chr22:29709800-29710600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood

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