Variant report

Variant	rs2773349
Chromosome Location	chr9:100398254-100398255
allele	C/T
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	TBL1XR1	chr9:100398146-100398302	K562	blood:	n/a	n/a
2	FOXA1	chr9:100398202-100398439	HepG2	liver:	n/a	n/a
3	WRNIP1	chr9:100398254-100398361	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100394431..100399065-chr9:100743200..100747046,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TSTD2-1	chr9:100398245-100398333	ENSG00000231521.1

Variant related genes	Relation type
TSTD2	TF binding region
ENSG00000136938	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1962592	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2149984	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245694	0.90[EUR][1000 genomes]
rs2254733	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2773343	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773344	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773350	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773354	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2773358	0.94[EUR][1000 genomes]
rs2805774	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805785	0.90[EUR][1000 genomes]
rs2805786	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805787	0.89[EUR][1000 genomes]
rs2805788	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805792	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805793	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805802	0.82[EUR][1000 genomes]
rs2805831	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2805834	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2808669	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2808676	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7863516	0.88[ASN][1000 genomes]
rs932916	0.87[EUR][1000 genomes];0.88[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	nsv1039240	chr9:100292680-100415269	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv540179	chr9:100292680-100415269	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking 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	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100394200-100398600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr9:100394400-100399200	Active TSS	Right Atrium	heart
3	chr9:100394600-100399200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:100396600-100398400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr9:100396600-100398600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:100396800-100398400	Enhancers	Spleen	Spleen
7	chr9:100396800-100399000	Weak transcription	Aorta	Aorta
8	chr9:100396800-100400600	Weak transcription	Gastric	stomach
9	chr9:100396800-100410200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:100397000-100398400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr9:100397000-100398400	Enhancers	Primary B cells from peripheral blood	blood
12	chr9:100397000-100398400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr9:100397000-100398400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:100397000-100398600	Enhancers	Fetal Heart	heart
15	chr9:100397000-100399600	Enhancers	Stomach Mucosa	stomach
16	chr9:100397000-100403000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr9:100397000-100405800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:100397000-100409200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr9:100397000-100410200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:100397000-100410200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:100397000-100411000	Weak transcription	Esophagus	oesophagus
22	chr9:100397200-100398400	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr9:100397200-100398400	Enhancers	Primary B cells from cord blood	blood
24	chr9:100397200-100398400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:100397200-100398400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:100397200-100398400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:100397200-100398400	Transcr. at gene 5' and 3'	Dnd41	blood
28	chr9:100397200-100398600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr9:100397200-100399000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr9:100397200-100399400	Enhancers	Primary hematopoietic stem cells	blood
31	chr9:100397200-100399400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr9:100397200-100399400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr9:100397200-100400000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr9:100397200-100400200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr9:100397200-100405600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:100397400-100398400	Enhancers	Fetal Thymus	thymus
37	chr9:100397400-100398400	Flanking Active TSS	HepG2	liver
38	chr9:100397400-100398400	Transcr. at gene 5' and 3'	HSMM	muscle
39	chr9:100397400-100398600	Enhancers	Colon Smooth Muscle	Colon
40	chr9:100397400-100398600	Enhancers	Fetal Lung	lung
41	chr9:100397400-100399000	Weak transcription	Right Ventricle	heart
42	chr9:100397400-100399400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:100397400-100399400	Enhancers	Small Intestine	intestine
44	chr9:100397400-100400000	Enhancers	Adipose Nuclei	Adipose
45	chr9:100397400-100401600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr9:100397400-100401800	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr9:100397400-100402000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr9:100397400-100403000	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr9:100397600-100398400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr9:100397600-100398400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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