Variant report

Variant	rs129889
Chromosome Location	chr9:136542868-136542869
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136533491..136538951-chr9:136540367..136544630,5	MCF-7	breast:
2	chr9:136541535..136544211-chr9:136557001..136558713,2	K562	blood:
3	chr9:136541535..136543901-chr9:136557001..136558944,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1076149	0.89[JPT][hapmap]
rs129890	0.95[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs129891	0.87[ASN][1000 genomes]
rs129892	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs129893	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs129895	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs129900	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs129901	0.82[JPT][hapmap]
rs129903	0.87[CHB][hapmap]
rs129904	0.83[CHB][hapmap]
rs129905	0.83[CHB][hapmap]
rs129907	0.83[CHB][hapmap]
rs129939	0.84[ASN][1000 genomes]
rs129957	0.86[ASN][1000 genomes]
rs1548362	0.87[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2519072	0.87[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2519120	0.89[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2519126	0.87[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs2519130	0.81[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2519131	0.84[ASN][1000 genomes]
rs2797830	0.87[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2797831	0.95[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap]
rs2797832	0.88[ASN][1000 genomes]
rs35138178	0.87[ASN][1000 genomes]
rs4744533	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs733149	0.83[CHB][hapmap]
rs756682	0.83[CHB][hapmap]
rs756687	0.84[JPT][hapmap]
rs756690	0.83[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs756691	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894081	chr9:136227260-136678954	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv894086	chr9:136281753-136657960	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv530972	chr9:136324358-136643044	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv894100	chr9:136371224-136547602	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv870051	chr9:136459745-136656889	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv894106	chr9:136489539-136566959	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv894107	chr9:136494566-136579589	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv894108	chr9:136507473-136617292	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv894110	chr9:136512515-136542868	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv894111	chr9:136522985-136563926	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv894112	chr9:136528721-136571089	Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1049434	chr9:136529766-136618314	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription 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	7 gene(s)	inside rSNPs	diseases
13	esv1793889	chr9:136533509-136581419	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1049281	chr9:136535471-136617805	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv894113	chr9:136538798-136586367	Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv894114	chr9:136538798-136779153	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
17	nsv428546	chr9:136541745-136720872	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs129889	CEL	cis	cerebellum	SCAN
rs129889	GFI1B	cis	cerebellum	SCAN
rs129889	BAT2L1	cis	cerebellum	SCAN
rs129889	CAMSAP1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136524800-136555600	Weak transcription	HSMM	muscle
2	chr9:136525000-136556800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr9:136528600-136544200	Weak transcription	Ovary	ovary
4	chr9:136530800-136561000	Weak transcription	Gastric	stomach
5	chr9:136532000-136543600	Weak transcription	Lung	lung
6	chr9:136538400-136548200	Weak transcription	Pancreas	Pancrea
7	chr9:136538600-136544600	Weak transcription	Right Ventricle	heart
8	chr9:136538600-136549000	Weak transcription	Fetal Brain Female	brain
9	chr9:136539000-136543800	Weak transcription	Fetal Lung	lung
10	chr9:136539200-136544000	Weak transcription	Fetal Heart	heart
11	chr9:136539800-136546000	Enhancers	Primary T cells fromperipheralblood	blood
12	chr9:136540000-136546600	Weak transcription	HepG2	liver
13	chr9:136540000-136548400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr9:136540200-136549200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:136540600-136543600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr9:136540600-136544000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr9:136540600-136544200	Enhancers	Primary T cells from cord blood	blood
18	chr9:136540800-136543600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr9:136540800-136544200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr9:136540800-136544400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr9:136540800-136544400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr9:136541200-136543200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr9:136541200-136543600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr9:136541400-136545000	Enhancers	Fetal Thymus	thymus
25	chr9:136541600-136543400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:136541600-136545800	Enhancers	Fetal Muscle Leg	muscle
27	chr9:136541600-136551000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr9:136542000-136544200	Enhancers	Thymus	Thymus
29	chr9:136542000-136544600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:136542000-136548200	Strong transcription	Liver	Liver
31	chr9:136542400-136543000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr9:136542400-136543000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr9:136542400-136543200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:136542400-136543200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr9:136542400-136544000	Enhancers	Primary hematopoietic stem cells	blood
36	chr9:136542400-136545600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr9:136542600-136543200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr9:136542600-136543200	Weak transcription	Spleen	Spleen
39	chr9:136542600-136544200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:136542800-136543200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:136542800-136543200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr9:136542800-136543200	Enhancers	Right Atrium	heart
43	chr9:136542800-136548200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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