Variant report

Variant	rs9556494
Chromosome Location	chr13:96332300-96332301
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	CHD1	chr13:96332286-96332313	GM12878	blood:	n/a	n/a
2	RCOR1	chr13:96332272-96332451	K562	blood:	n/a	n/a
3	POLR2A	chr13:96332202-96332362	K562	blood:	n/a	n/a
4	ARID3A	chr13:96332080-96332568	K562	blood:	n/a	n/a
5	IRF1	chr13:96332199-96332586	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96327839..96330034-chr13:96330873..96332549,2	MCF-7	breast:

Variant related genes	Relation type
DNAJC3-AS1	TF binding region
ENSG00000247400	Chromatin interaction
ENSG00000102580	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12583253	0.82[ASN][1000 genomes]
rs12583374	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12585001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12585954	1.00[AFR][1000 genomes]
rs17881101	0.82[ASN][1000 genomes]
rs17882362	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289812	0.82[ASN][1000 genomes]
rs2289813	0.82[ASN][1000 genomes]
rs3759446	0.83[EUR][1000 genomes]
rs3848075	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58498169	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60253451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72632666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72632667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9556498	0.82[ASN][1000 genomes]
rs9561922	0.81[EUR][1000 genomes]
rs9561933	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9561938	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9561944	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9561952	0.82[ASN][1000 genomes]
rs9561954	0.82[ASN][1000 genomes]
rs9561958	0.82[ASN][1000 genomes]
rs9669929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832690	chr13:96330757-96508077	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96325600-96332400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:96329600-96332400	Active TSS	Right Atrium	heart
3	chr13:96330200-96333200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr13:96330200-96340800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:96330600-96332400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr13:96330600-96336400	Weak transcription	Gastric	stomach
7	chr13:96330600-96336800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:96330600-96340800	Weak transcription	Spleen	Spleen
9	chr13:96330800-96332400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr13:96330800-96332400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr13:96330800-96333600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr13:96330800-96333800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr13:96330800-96334400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr13:96330800-96334400	Weak transcription	Fetal Brain Female	brain
15	chr13:96330800-96336000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr13:96330800-96336800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr13:96330800-96337000	Weak transcription	Lung	lung
18	chr13:96331000-96333400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr13:96331000-96336400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr13:96331000-96336400	Weak transcription	Fetal Stomach	stomach
21	chr13:96331200-96332400	Enhancers	Fetal Heart	heart
22	chr13:96331200-96332600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr13:96331200-96332600	Enhancers	Fetal Intestine Large	intestine
24	chr13:96331200-96332600	Enhancers	Fetal Lung	lung
25	chr13:96331200-96333000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr13:96331200-96333000	Enhancers	Liver	Liver
27	chr13:96331200-96333200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr13:96331200-96335000	Weak transcription	Fetal Muscle Leg	muscle
29	chr13:96331200-96336400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr13:96331200-96336800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr13:96331200-96336800	Weak transcription	Fetal Intestine Small	intestine
32	chr13:96331200-96336800	Weak transcription	Placenta	Placenta
33	chr13:96331200-96337000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr13:96331200-96339400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr13:96331400-96332400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr13:96331400-96332400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr13:96331400-96332400	Enhancers	Brain Hippocampus Middle	brain
38	chr13:96331400-96332600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr13:96331400-96332600	Enhancers	HUVEC	blood vessel
40	chr13:96331400-96332600	Enhancers	Osteobl	bone
41	chr13:96331400-96333200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr13:96331400-96333400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr13:96331400-96333600	Enhancers	Primary T cells from cord blood	blood
44	chr13:96331400-96333600	Weak transcription	Pancreas	Pancrea
45	chr13:96331400-96334000	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr13:96331400-96335000	Enhancers	HepG2	liver
47	chr13:96331400-96336400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr13:96331400-96336400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr13:96331400-96336400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr13:96331400-96336400	Weak transcription	Brain Inferior Temporal Lobe	brain

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