Variant report

Variant	rs1322250
Chromosome Location	chr9:5435709-5435710
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	chr9:5434272..5436176-chr9:5438552..5440389,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10739074	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10739075	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10758688	0.84[EUR][1000 genomes]
rs10758689	0.82[EUR][1000 genomes]
rs10815221	0.84[EUR][1000 genomes]
rs10815222	0.84[EUR][1000 genomes]
rs10815223	0.95[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10975112	0.90[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs10975113	0.82[EUR][1000 genomes]
rs10975114	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10975116	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2093455	0.81[EUR][1000 genomes]
rs2093456	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2295870	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3780392	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4742092	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7023253	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7862054	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892136	chr9:4921639-5436461	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv529689	chr9:4970093-5483250	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv892141	chr9:5116616-5479822	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1017126	chr9:5117847-5695486	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv539964	chr9:5117847-5695486	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv949627	chr9:5174829-5712626	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv427837	chr9:5189756-5454512	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	esv2759660	chr9:5288908-5454512	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	esv2758177	chr9:5297921-5454512	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv466108	chr9:5345673-5514372	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
11	nsv613196	chr9:5345673-5514372	Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	esv3330820	chr9:5366750-5510260	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5376000-5436800	Weak transcription	Psoas Muscle	Psoas
2	chr9:5409800-5436400	Weak transcription	Small Intestine	intestine
3	chr9:5415400-5437000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:5418400-5436600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr9:5419200-5437000	Weak transcription	Aorta	Aorta
6	chr9:5419200-5437000	Weak transcription	Pancreas	Pancrea
7	chr9:5420000-5436800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr9:5425400-5435800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr9:5426200-5436400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr9:5427600-5436000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr9:5428000-5436600	Strong transcription	Fetal Muscle Trunk	muscle
12	chr9:5428200-5436000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr9:5429400-5435800	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr9:5429600-5436600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:5430400-5436600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr9:5430600-5436400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:5430800-5436000	Weak transcription	Brain Substantia Nigra	brain
18	chr9:5430800-5436600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr9:5431200-5437000	Weak transcription	Brain Anterior Caudate	brain
20	chr9:5431800-5435800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:5431800-5436800	Weak transcription	Right Atrium	heart
22	chr9:5432000-5436400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr9:5432400-5435800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr9:5432400-5437200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:5433000-5435800	Weak transcription	Stomach Mucosa	stomach
26	chr9:5433400-5435800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr9:5433400-5436000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:5433600-5436800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr9:5433800-5436400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:5433800-5436600	Weak transcription	NHLF	lung
31	chr9:5434000-5437000	Weak transcription	Colonic Mucosa	Colon
32	chr9:5434200-5435800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:5434200-5436200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr9:5434200-5437000	Weak transcription	Fetal Brain Female	brain
35	chr9:5434400-5435800	Strong transcription	Left Ventricle	heart
36	chr9:5434400-5436200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:5434400-5436400	Strong transcription	Brain Hippocampus Middle	brain
38	chr9:5434600-5435800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:5434600-5436000	Strong transcription	Fetal Muscle Leg	muscle
40	chr9:5434600-5436200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr9:5434600-5436400	Weak transcription	NH-A	brain
42	chr9:5434800-5435800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:5434800-5435800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr9:5434800-5435800	Weak transcription	Gastric	stomach
45	chr9:5434800-5435800	Weak transcription	Lung	lung
46	chr9:5434800-5436000	Weak transcription	NHDF-Ad	bronchial
47	chr9:5434800-5436200	Strong transcription	Fetal Intestine Large	intestine
48	chr9:5434800-5436200	Weak transcription	Fetal Intestine Small	intestine
49	chr9:5434800-5436400	Weak transcription	Spleen	Spleen
50	chr9:5434800-5436600	Weak transcription	Primary monocytes fromperipheralblood	blood

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