Variant report

Variant	rs474845
Chromosome Location	chr9:3244462-3244463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:3239523..3241471-chr9:3244175..3245979,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1147822	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs11998979	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs12004313	0.85[ASN][1000 genomes]
rs12004744	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs16916423	0.85[CEU][hapmap]
rs17658838	0.85[CEU][hapmap]
rs17715051	0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs2986690	0.86[CEU][hapmap]
rs2986697	0.83[CEU][hapmap]
rs2991297	0.86[CEU][hapmap]
rs2991298	0.84[CEU][hapmap]
rs3012686	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs3012688	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs3012693	0.85[CEU][hapmap]
rs472139	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490961	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs494348	0.82[EUR][1000 genomes]
rs506149	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs527697	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs535305	0.81[EUR][1000 genomes]
rs535614	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs540859	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs594370	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs612198	0.88[ASN][1000 genomes]
rs617047	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs617992	0.85[CEU][hapmap]
rs619401	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs625941	0.86[CEU][hapmap]
rs633893	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs636548	0.85[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs645583	0.84[CHB][hapmap];0.87[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs646529	0.83[EUR][1000 genomes]
rs649990	0.86[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs656686	0.86[CEU][hapmap]
rs658123	0.85[CEU][hapmap]
rs72699004	0.88[ASN][1000 genomes]
rs7850999	0.85[CEU][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7866129	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7868041	0.90[ASN][1000 genomes]
rs7873658	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1017474	chr9:3019068-3247215	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1028668	chr9:3139007-3262791	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv539939	chr9:3139007-3262791	Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv466090	chr9:3237378-3349487	Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv613145	chr9:3237378-3349487	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3217200-3245200	Weak transcription	Left Ventricle	heart
2	chr9:3220000-3256600	Weak transcription	Brain Anterior Caudate	brain
3	chr9:3220400-3287400	Weak transcription	Psoas Muscle	Psoas
4	chr9:3221800-3251400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:3221800-3256400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:3222000-3246400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr9:3222000-3247800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr9:3222200-3256200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:3222200-3269400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr9:3222400-3247400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr9:3222400-3254800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:3223200-3246400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr9:3223200-3254800	Weak transcription	Brain Angular Gyrus	brain
14	chr9:3223200-3277000	Weak transcription	HSMMtube	muscle
15	chr9:3223400-3246000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr9:3223400-3270200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:3223600-3246400	Weak transcription	Fetal Intestine Large	intestine
18	chr9:3223600-3247800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr9:3223600-3255400	Weak transcription	Right Ventricle	heart
20	chr9:3223600-3256600	Weak transcription	Thymus	Thymus
21	chr9:3223600-3264400	Weak transcription	Fetal Intestine Small	intestine
22	chr9:3223600-3271600	Weak transcription	Lung	lung
23	chr9:3223600-3284800	Weak transcription	Spleen	Spleen
24	chr9:3224000-3275800	Weak transcription	Gastric	stomach
25	chr9:3225200-3262800	Weak transcription	Esophagus	oesophagus
26	chr9:3225400-3247800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:3225800-3255600	Weak transcription	Fetal Stomach	stomach
28	chr9:3226600-3289600	Weak transcription	Colon Smooth Muscle	Colon
29	chr9:3226800-3246600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr9:3227400-3256600	Weak transcription	Brain Hippocampus Middle	brain
31	chr9:3230000-3254200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr9:3232000-3253200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr9:3232000-3254600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr9:3232200-3246200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr9:3232400-3246400	Weak transcription	Adipose Nuclei	Adipose
36	chr9:3232400-3256400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr9:3233600-3256400	Weak transcription	Brain Substantia Nigra	brain
38	chr9:3233600-3292600	Weak transcription	Pancreas	Pancrea
39	chr9:3234000-3256400	Weak transcription	Liver	Liver
40	chr9:3234800-3294400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:3235800-3247400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr9:3235800-3269800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr9:3236000-3255200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr9:3236200-3247400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr9:3236200-3271600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr9:3236800-3246400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:3236800-3247400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr9:3236800-3254800	Weak transcription	Brain Germinal Matrix	brain
49	chr9:3236800-3254800	Weak transcription	Ovary	ovary
50	chr9:3236800-3256400	Weak transcription	Fetal Brain Female	brain

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