Variant report

Variant	rs3108
Chromosome Location	chr13:40129529-40129530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11618841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11619569	0.99[ASN][1000 genomes]
rs11619916	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12428145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1475177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17060207	1.00[ASN][1000 genomes]
rs17060285	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2324334	1.00[ASN][1000 genomes]
rs2324336	0.92[JPT][hapmap]
rs2324338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2324341	0.96[CEU][hapmap];0.88[CHB][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56066871	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563724	0.99[ASN][1000 genomes]
rs6563725	0.99[ASN][1000 genomes]
rs7324765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73466835	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7987701	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7992600	0.99[ASN][1000 genomes]
rs7998105	0.92[ASN][1000 genomes]
rs7998772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8000770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548814	0.81[JPT][hapmap]
rs9594342	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9603561	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603563	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9603565	0.95[CEU][hapmap];0.94[CHB][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs967401	0.95[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40107800-40140200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr13:40111200-40133200	Weak transcription	Aorta	Aorta
3	chr13:40114000-40131200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr13:40114400-40136000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr13:40115400-40133200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr13:40115600-40133600	Weak transcription	Osteobl	bone
7	chr13:40117000-40130000	Weak transcription	Fetal Muscle Leg	muscle
8	chr13:40117000-40130400	Weak transcription	HSMMtube	muscle
9	chr13:40117800-40131200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr13:40119800-40130200	Weak transcription	Fetal Heart	heart
11	chr13:40120000-40131600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr13:40121400-40136200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr13:40123000-40131800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr13:40125000-40131600	Weak transcription	Fetal Lung	lung
15	chr13:40125400-40133400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr13:40125600-40131400	Weak transcription	HSMM	muscle
17	chr13:40125600-40133000	Weak transcription	Lung	lung
18	chr13:40125800-40130000	Weak transcription	Adipose Nuclei	Adipose
19	chr13:40126400-40137200	Weak transcription	NHLF	lung
20	chr13:40126600-40130200	Weak transcription	Right Ventricle	heart
21	chr13:40126800-40130600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr13:40127000-40131200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr13:40127000-40133400	Weak transcription	Brain Angular Gyrus	brain
24	chr13:40127000-40136200	Weak transcription	NHDF-Ad	bronchial
25	chr13:40128600-40129600	Enhancers	Ovary	ovary
26	chr13:40128800-40130400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:40128800-40137600	Weak transcription	Colon Smooth Muscle	Colon
28	chr13:40129000-40130000	Weak transcription	Right Atrium	heart
29	chr13:40129000-40131400	Weak transcription	Left Ventricle	heart
30	chr13:40129000-40131800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr13:40129000-40133000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr13:40129000-40133200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr13:40129000-40145600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr13:40129000-40152800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr13:40129200-40133200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr13:40129200-40133200	Weak transcription	Brain Substantia Nigra	brain
37	chr13:40129200-40135800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr13:40129200-40135800	Weak transcription	HMEC	breast
39	chr13:40129400-40136800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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