Variant report

Variant	rs498769
Chromosome Location	chr13:39981451-39981452
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:39943129..39945538-chr13:39980519..39982065,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1185801	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1186156	0.93[EUR][1000 genomes]
rs1186157	0.94[ASW][hapmap]
rs1535778	0.82[CHB][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes]
rs1927200	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479090	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941926	0.88[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.95[AFR][1000 genomes]
rs4943661	0.83[EUR][1000 genomes]
rs626904	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs671316	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1036674	chr13:39841482-40008117	Bivalent Enhancer Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv900008	chr13:39962791-40020267	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39972800-39988600	Weak transcription	Fetal Muscle Leg	muscle
2	chr13:39975800-39988400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:39975800-39988600	Weak transcription	Right Atrium	heart
4	chr13:39976200-39984000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr13:39976600-39990600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:39977000-39987800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:39977200-39983800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr13:39977400-39983600	Weak transcription	Brain Hippocampus Middle	brain
9	chr13:39977600-39982600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr13:39977800-39984400	Weak transcription	Psoas Muscle	Psoas
11	chr13:39979200-39981800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr13:39979400-39981600	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr13:39979400-39983600	Weak transcription	Fetal Brain Male	brain
14	chr13:39979600-39981600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr13:39980000-39983600	Weak transcription	Brain Anterior Caudate	brain
16	chr13:39980000-39983600	Weak transcription	Fetal Lung	lung
17	chr13:39980000-39983800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:39980000-39983800	Weak transcription	NHDF-Ad	bronchial
19	chr13:39980000-39984000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:39980000-39984000	Weak transcription	NHLF	lung
21	chr13:39980200-39982400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr13:39980200-39983200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr13:39980200-39983200	Weak transcription	Brain Angular Gyrus	brain
24	chr13:39980200-39983600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr13:39980200-39983600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr13:39980200-39983800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr13:39980200-39984400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr13:39980200-39988600	Weak transcription	Fetal Stomach	stomach
29	chr13:39980400-39982000	Weak transcription	Fetal Heart	heart
30	chr13:39980400-39983600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr13:39980400-39983800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr13:39980400-39984400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr13:39980800-39981600	Enhancers	HMEC	breast
34	chr13:39980800-39984600	Weak transcription	HSMM	muscle
35	chr13:39981000-39981600	Enhancers	Brain Substantia Nigra	brain
36	chr13:39981000-39981600	Enhancers	Ovary	ovary
37	chr13:39981000-39981600	Enhancers	Right Ventricle	heart
38	chr13:39981000-39981800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr13:39981000-39983400	Enhancers	Left Ventricle	heart
40	chr13:39981400-39981600	Enhancers	HUVEC	blood vessel
41	chr13:39981400-39981800	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr13:39981400-39982600	Enhancers	Brain Cingulate Gyrus	brain
43	chr13:39981400-39991800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr13:39981400-39991800	Weak transcription	NHEK	skin

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