Variant report

Variant	rs886016
Chromosome Location	chr9:136555629-136555630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136553976..136556938-chr9:136571128..136573086,2	MCF-7	breast:
2	chr9:136539587..136542544-chr9:136554397..136556598,2	MCF-7	breast:
3	chr9:136547609..136549609-chr9:136554134..136556211,2	MCF-7	breast:
4	chr9:136510698..136512936-chr9:136554635..136557267,2	MCF-7	breast:
5	chr9:136549300..136551491-chr9:136553911..136555708,2	K562	blood:
6	chr9:136551308..136553495-chr9:136555046..136558031,3	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1076149	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs129891	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs129892	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs129893	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs129894	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs129895	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs129896	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs129897	0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs129898	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs129899	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs129900	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs129901	1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs129903	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs129904	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs129905	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs129906	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs129907	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs129939	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs129948	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs129951	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs129957	0.87[ASN][1000 genomes]
rs1548362	0.91[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1548363	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073816	0.96[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2073817	0.92[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2502734	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2502736	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2519071	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2519072	0.87[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2519120	0.90[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2519126	0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2519129	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2519130	0.95[CHB][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2519131	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2797820	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2797823	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2797829	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2797830	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2797831	0.81[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap]
rs2797832	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35138178	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4744533	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs730007	0.88[CEU][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs733149	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs756682	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs756687	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs756690	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs756691	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv466620	chr9:136550817-136571089	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv615689	chr9:136550817-136571089	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv469907	chr9:136552263-136600201	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs886016	GBGT1	cis	cerebellum	SCAN
rs886016	CAMSAP1	cis	cerebellum	SCAN
rs886016	CEL	cis	cerebellum	SCAN
rs886016	UCK1	cis	parietal	SCAN
rs886016	BAT2L1	cis	cerebellum	SCAN
rs886016	GFI1B	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136525000-136556800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr9:136530800-136561000	Weak transcription	Gastric	stomach
3	chr9:136545400-136559600	Weak transcription	Fetal Heart	heart
4	chr9:136545600-136557800	Weak transcription	Ovary	ovary
5	chr9:136545600-136567600	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:136548800-136556400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:136549000-136556200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:136549400-136556600	Weak transcription	Brain Anterior Caudate	brain
9	chr9:136549600-136566800	Weak transcription	Spleen	Spleen
10	chr9:136549800-136558400	Weak transcription	Fetal Thymus	thymus
11	chr9:136550000-136556000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:136550000-136559200	Weak transcription	Thymus	Thymus
13	chr9:136550000-136564800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr9:136550000-136566200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr9:136550200-136565800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:136550200-136567600	Weak transcription	Right Atrium	heart
17	chr9:136550400-136558200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr9:136550600-136558800	Weak transcription	Pancreas	Pancrea
19	chr9:136550600-136562800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:136550800-136555800	Weak transcription	Brain Germinal Matrix	brain
21	chr9:136550800-136563400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr9:136551400-136562200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr9:136551600-136556400	Weak transcription	Brain Substantia Nigra	brain
24	chr9:136552000-136556400	Weak transcription	Brain Hippocampus Middle	brain
25	chr9:136552200-136556400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr9:136552200-136556400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:136552200-136556600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr9:136552200-136566000	Weak transcription	Lung	lung
29	chr9:136552200-136567600	Weak transcription	Fetal Kidney	kidney
30	chr9:136552400-136556400	Weak transcription	Brain Angular Gyrus	brain
31	chr9:136552400-136561600	Strong transcription	Primary T cells from cord blood	blood
32	chr9:136553400-136558000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:136553600-136561600	Strong transcription	Fetal Stomach	stomach
34	chr9:136553600-136562600	Strong transcription	Liver	Liver
35	chr9:136554000-136557600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:136554200-136560400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr9:136554400-136556000	Strong transcription	HepG2	liver
38	chr9:136554600-136558000	Enhancers	Placenta Amnion	Placenta Amnion
39	chr9:136554800-136556800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr9:136554800-136558400	Weak transcription	Fetal Intestine Small	intestine
41	chr9:136554800-136561200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr9:136555000-136556400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr9:136555000-136557000	Enhancers	Fetal Lung	lung
44	chr9:136555000-136557200	Enhancers	Placenta	Placenta
45	chr9:136555000-136557400	Enhancers	HSMMtube	muscle
46	chr9:136555200-136556000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr9:136555200-136557400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:136555400-136556400	Weak transcription	NH-A	brain
49	chr9:136555400-136557400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:136555400-136558600	Weak transcription	Fetal Muscle Leg	muscle

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