Variant report

Variant	rs13296447
Chromosome Location	chr9:101833187-101833188
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101551519..101553128-chr9:101832657..101834738,2	K562	blood:

Variant related genes	Relation type
ENSG00000165138	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1051105	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10988700	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11788920	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12683114	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12685226	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1413298	0.81[CHB][hapmap];0.93[CHD][hapmap];0.83[LWK][hapmap];0.94[MKK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1537504	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16918198	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34111295	0.80[AMR][1000 genomes]
rs34863444	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35312758	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4480177	0.81[AMR][1000 genomes]
rs4742756	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4742758	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4742759	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4742760	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4742761	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4743321	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4743322	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4743323	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743324	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4743325	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57992539	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7022000	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7025264	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7030799	0.86[YRI][hapmap];0.80[AMR][1000 genomes]
rs7031364	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7031588	0.82[MEX][hapmap];0.90[MKK][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs7046702	0.95[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7047475	0.85[YRI][hapmap];0.80[AMR][1000 genomes]
rs71494009	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7874183	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs885154	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs885155	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914991	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs914992	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][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	nsv893618	chr9:101800106-101886071	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13296447	TSTD2	cis	parietal	SCAN
rs13296447	COL15A1	cis	lymphoblastoid	seeQTL
rs13296447	C9orf102	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101793800-101837600	Weak transcription	Psoas Muscle	Psoas
2	chr9:101816200-101844200	Weak transcription	Gastric	stomach
3	chr9:101818000-101834800	Weak transcription	Pancreas	Pancrea
4	chr9:101821800-101834800	Strong transcription	Stomach Smooth Muscle	stomach
5	chr9:101822000-101834000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:101822400-101837600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr9:101822400-101838600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:101824000-101833200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr9:101825200-101836200	Weak transcription	Fetal Brain Female	brain
10	chr9:101826600-101833200	Weak transcription	Right Ventricle	heart
11	chr9:101826600-101848200	Weak transcription	Aorta	Aorta
12	chr9:101828600-101837000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr9:101828800-101833200	Weak transcription	Right Atrium	heart
14	chr9:101829000-101834600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr9:101829600-101833400	Weak transcription	K562	blood
16	chr9:101829600-101834800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:101829800-101833200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:101830000-101837600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:101830800-101833200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr9:101830800-101833400	Enhancers	Primary T cells from cord blood	blood
21	chr9:101830800-101833400	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr9:101831000-101834600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr9:101831200-101839000	Weak transcription	Colonic Mucosa	Colon
24	chr9:101831600-101833400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:101831600-101834600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr9:101831600-101834600	Enhancers	NHLF	lung
27	chr9:101831800-101833200	Weak transcription	Left Ventricle	heart
28	chr9:101831800-101833200	Weak transcription	HSMMtube	muscle
29	chr9:101831800-101837000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:101831800-101837000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:101831800-101838400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:101832000-101834200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:101832000-101834600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:101832000-101837200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr9:101832200-101833200	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr9:101832200-101833400	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:101832200-101833800	Weak transcription	HUVEC	blood vessel
38	chr9:101832200-101834000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr9:101832200-101834000	Weak transcription	Placenta	Placenta
40	chr9:101832200-101834200	Enhancers	Osteobl	bone
41	chr9:101832200-101835200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr9:101832200-101836600	Weak transcription	Thymus	Thymus
43	chr9:101832200-101836600	Weak transcription	Dnd41	blood
44	chr9:101832200-101837000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr9:101832200-101837600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr9:101832200-101837800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr9:101832200-101839200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr9:101832400-101833400	Enhancers	NHDF-Ad	bronchial
49	chr9:101832400-101833800	Genic enhancers	Adipose Nuclei	Adipose
50	chr9:101832400-101834000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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