Variant report

Variant	rs1408606
Chromosome Location	chr13:96277926-96277927
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	chr13:96277245..96279112-chr13:96327226..96329266,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247400	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1000600	0.88[CHB][hapmap]
rs11070146	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070147	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1535990	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17235320	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs2038782	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3742150	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4143093	0.87[CHB][hapmap]
rs4497528	0.94[CHB][hapmap]
rs4773921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329790	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7334692	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7338545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7986280	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7989079	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9302082	0.94[CHB][hapmap]
rs9525034	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9590305	0.94[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900934	chr13:96255706-96327574	Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96235600-96284200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr13:96246400-96278600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr13:96247800-96293600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:96251400-96294400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr13:96256400-96295200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr13:96256800-96294200	Weak transcription	Placenta	Placenta
7	chr13:96260200-96279000	Weak transcription	Liver	Liver
8	chr13:96260200-96293400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr13:96260600-96279200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr13:96261200-96288400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr13:96262000-96280800	Weak transcription	Fetal Heart	heart
12	chr13:96262800-96278000	Strong transcription	HSMM	muscle
13	chr13:96263600-96290000	Weak transcription	Adipose Nuclei	Adipose
14	chr13:96265800-96293400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr13:96266400-96286000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr13:96267600-96293000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr13:96267800-96278000	Strong transcription	NH-A	brain
18	chr13:96268000-96279400	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr13:96268400-96286400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:96268400-96291600	Strong transcription	Osteobl	bone
21	chr13:96268800-96281400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr13:96270200-96293400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr13:96270600-96280200	Weak transcription	Aorta	Aorta
24	chr13:96271600-96284800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr13:96272400-96292000	Weak transcription	Colonic Mucosa	Colon
26	chr13:96272600-96284000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr13:96273000-96287400	Strong transcription	Fetal Lung	lung
28	chr13:96273400-96279000	Weak transcription	Brain Anterior Caudate	brain
29	chr13:96273400-96281400	Weak transcription	Brain Hippocampus Middle	brain
30	chr13:96273400-96284000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr13:96273600-96293400	Weak transcription	Brain Substantia Nigra	brain
32	chr13:96273600-96293600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr13:96273600-96293600	Weak transcription	Left Ventricle	heart
34	chr13:96273800-96279200	Weak transcription	Brain Angular Gyrus	brain
35	chr13:96273800-96293600	Weak transcription	Gastric	stomach
36	chr13:96273800-96293600	Weak transcription	Pancreas	Pancrea
37	chr13:96274000-96280000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr13:96274000-96281400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr13:96274200-96280800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr13:96274800-96280400	Weak transcription	Fetal Intestine Large	intestine
41	chr13:96275800-96278600	Weak transcription	NHDF-Ad	bronchial
42	chr13:96275800-96279000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr13:96275800-96279200	Weak transcription	Brain Germinal Matrix	brain
44	chr13:96275800-96279200	Weak transcription	Fetal Brain Male	brain
45	chr13:96275800-96279400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr13:96275800-96280200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr13:96275800-96280600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr13:96275800-96281000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr13:96275800-96281200	Weak transcription	HSMMtube	muscle
50	chr13:96276000-96279000	Weak transcription	A549	lung

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