Variant report

Variant	rs1537504
Chromosome Location	chr9:101829542-101829543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101828711..101831870-chr9:101834317..101838046,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1051105	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10988700	0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11788920	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12683114	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12685226	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13296447	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]
rs1413298	0.81[CHB][hapmap];0.93[CHD][hapmap];0.87[MKK][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs16918198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34863444	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35312758	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4742756	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742758	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742759	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742760	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742761	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4743321	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4743322	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743323	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4743324	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4743325	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57992539	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7022000	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7025264	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7031364	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7031588	0.85[GIH][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap]
rs7046702	0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71494009	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7874183	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs885154	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs885155	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs914991	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs914992	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.93[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
rs1537504	TSTD2	cis	parietal	SCAN
rs1537504	COL15A1	cis	lymphoblastoid	seeQTL
rs1537504	C9orf102	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101793800-101837600	Weak transcription	Psoas Muscle	Psoas
2	chr9:101807000-101831800	Strong transcription	Fetal Muscle Trunk	muscle
3	chr9:101807600-101831800	Strong transcription	Fetal Muscle Leg	muscle
4	chr9:101813200-101833000	Weak transcription	Lung	lung
5	chr9:101816200-101844200	Weak transcription	Gastric	stomach
6	chr9:101818000-101834800	Weak transcription	Pancreas	Pancrea
7	chr9:101820200-101831000	Weak transcription	Colonic Mucosa	Colon
8	chr9:101821800-101834800	Strong transcription	Stomach Smooth Muscle	stomach
9	chr9:101822000-101834000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:101822200-101832800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr9:101822400-101832400	Weak transcription	NHDF-Ad	bronchial
12	chr9:101822400-101837600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr9:101822400-101838600	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:101823000-101831400	Weak transcription	Thymus	Thymus
15	chr9:101823200-101831000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:101823400-101830800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr9:101823400-101831400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:101823400-101831600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr9:101823600-101830800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:101824000-101833200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr9:101824200-101831400	Strong transcription	Fetal Stomach	stomach
22	chr9:101824400-101831200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr9:101825200-101836200	Weak transcription	Fetal Brain Female	brain
24	chr9:101825600-101830600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr9:101825800-101830800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr9:101826000-101830800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr9:101826200-101830800	Weak transcription	Primary T cells from cord blood	blood
28	chr9:101826200-101830800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr9:101826600-101833200	Weak transcription	Right Ventricle	heart
30	chr9:101826600-101848200	Weak transcription	Aorta	Aorta
31	chr9:101826800-101831000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:101827000-101830800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr9:101827000-101832400	Strong transcription	Adipose Nuclei	Adipose
34	chr9:101827200-101830000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr9:101827600-101831400	Weak transcription	GM12878-XiMat	blood
36	chr9:101828000-101829600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:101828400-101829600	Enhancers	K562	blood
38	chr9:101828600-101832200	Strong transcription	Colon Smooth Muscle	Colon
39	chr9:101828600-101832400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:101828600-101837000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr9:101828800-101830000	Strong transcription	Rectal Smooth Muscle	rectum
42	chr9:101828800-101833000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:101828800-101833200	Weak transcription	Right Atrium	heart
44	chr9:101829000-101829600	Strong transcription	Left Ventricle	heart
45	chr9:101829000-101830000	Strong transcription	Ovary	ovary
46	chr9:101829000-101834600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:101829200-101831400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr9:101829200-101832200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr9:101829400-101829800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:101829400-101831000	Weak transcription	Primary T cells fromperipheralblood	blood

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