Variant report

Variant	rs2519129
Chromosome Location	chr9:136548340-136548341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136546579..136549426-chr9:136551457..136554920,3	K562	blood:
2	chr9:136547327..136548989-chr9:136894094..136896056,2	MCF-7	breast:
3	chr9:136547609..136549609-chr9:136554134..136556211,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235106	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1076149	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs129891	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs129892	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs129893	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs129894	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs129895	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs129896	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs129897	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs129898	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs129899	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs129900	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs129903	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs129905	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs129906	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs129907	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs129939	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs129948	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs129951	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs129957	0.91[ASN][1000 genomes]
rs1548362	0.93[ASN][1000 genomes]
rs1548363	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073816	0.85[ASN][1000 genomes]
rs2073817	0.82[ASN][1000 genomes]
rs2502734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2502736	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2519071	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2519072	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2519120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2519126	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2519130	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2519131	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2797820	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2797823	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2797829	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2797830	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2797832	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35138178	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4744533	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs730007	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs733149	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs756682	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs756687	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs756690	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs756691	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886016	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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

No data

Chromatin state (count:67 , 50 per page) page: 1 2

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	chr9:136530800-136561000	Weak transcription	Gastric	stomach
4	chr9:136538600-136549000	Weak transcription	Fetal Brain Female	brain
5	chr9:136540000-136548400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:136540200-136549200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:136541600-136551000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr9:136544200-136548600	Weak transcription	Thymus	Thymus
9	chr9:136544200-136549400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:136544600-136548400	Weak transcription	Fetal Intestine Large	intestine
11	chr9:136545000-136548400	Weak transcription	Brain Hippocampus Middle	brain
12	chr9:136545000-136548400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:136545200-136548800	Weak transcription	Brain Anterior Caudate	brain
14	chr9:136545400-136548400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:136545400-136559600	Weak transcription	Fetal Heart	heart
16	chr9:136545600-136557800	Weak transcription	Ovary	ovary
17	chr9:136545600-136567600	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:136545800-136548400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr9:136545800-136548400	Weak transcription	Fetal Brain Male	brain
20	chr9:136546200-136550600	Enhancers	Fetal Muscle Leg	muscle
21	chr9:136546400-136548400	Enhancers	Primary T cells from cord blood	blood
22	chr9:136546400-136548400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr9:136546400-136549400	Enhancers	Fetal Thymus	thymus
24	chr9:136546600-136548400	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr9:136546600-136549200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr9:136546600-136551400	Strong transcription	HepG2	liver
27	chr9:136546800-136548400	Enhancers	Primary T cells fromperipheralblood	blood
28	chr9:136547000-136548400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr9:136547200-136549000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr9:136547400-136548600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr9:136547400-136548800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr9:136547400-136549600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr9:136547400-136550000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr9:136547600-136549400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr9:136547600-136550000	Enhancers	Duodenum Mucosa	Duodenum
36	chr9:136547600-136551000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:136548000-136549000	Enhancers	Primary B cells from cord blood	blood
38	chr9:136548000-136549400	Enhancers	Primary B cells from peripheral blood	blood
39	chr9:136548000-136549600	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr9:136548000-136550000	Bivalent Enhancer	Placenta	Placenta
41	chr9:136548200-136548600	Weak transcription	Liver	Liver
42	chr9:136548200-136548600	Enhancers	Pancreas	Pancrea
43	chr9:136548200-136548800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:136548200-136548800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:136548200-136548800	Enhancers	Esophagus	oesophagus
46	chr9:136548200-136548800	Enhancers	Stomach Smooth Muscle	stomach
47	chr9:136548200-136549000	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr9:136548200-136549200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr9:136548200-136549200	Enhancers	Left Ventricle	heart
50	chr9:136548200-136549400	Enhancers	Brain Substantia Nigra	brain

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