Variant report

Variant	rs2324341
Chromosome Location	chr13:40142454-40142455
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11618841	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11619569	0.84[ASN][1000 genomes]
rs12428145	0.96[CEU][hapmap];0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1475177	0.95[CEU][hapmap];0.88[CHB][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17060207	0.85[ASN][1000 genomes]
rs17060285	0.83[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2324334	0.85[ASN][1000 genomes]
rs2324338	0.95[CEU][hapmap];0.88[CHB][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3108	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	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59443260	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6563724	0.84[ASN][1000 genomes]
rs6563725	0.84[ASN][1000 genomes]
rs7324765	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73466835	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7987701	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7992600	0.84[ASN][1000 genomes]
rs7998772	0.88[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8000770	0.95[CEU][hapmap];0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9594342	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9603561	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9603563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs967401	1.00[CEU][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes];0.99[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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40129000-40145600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:40129000-40152800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:40132200-40145600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr13:40135800-40145600	Weak transcription	Lung	lung
5	chr13:40136400-40145600	Weak transcription	Right Ventricle	heart
6	chr13:40138800-40152800	Weak transcription	Aorta	Aorta
7	chr13:40139200-40158000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr13:40139800-40146400	Weak transcription	Brain Substantia Nigra	brain
9	chr13:40140000-40145600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:40140000-40169400	Weak transcription	Fetal Stomach	stomach
11	chr13:40140200-40145600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr13:40140200-40149600	Weak transcription	Fetal Muscle Leg	muscle
13	chr13:40140400-40145400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:40140400-40157800	Weak transcription	Adipose Nuclei	Adipose
15	chr13:40140600-40143000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr13:40140600-40144400	Weak transcription	Fetal Heart	heart
17	chr13:40140600-40145200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:40140600-40146600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:40140600-40148600	Weak transcription	Fetal Lung	lung
20	chr13:40140800-40142800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr13:40140800-40142800	Weak transcription	Left Ventricle	heart
22	chr13:40140800-40142800	Weak transcription	Ovary	ovary
23	chr13:40140800-40143200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr13:40140800-40145400	Weak transcription	Right Atrium	heart
25	chr13:40140800-40152800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr13:40140800-40165400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr13:40141200-40142800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr13:40141200-40145600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr13:40141200-40145600	Weak transcription	NHLF	lung
30	chr13:40141400-40143200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr13:40141400-40143200	Enhancers	HMEC	breast
32	chr13:40142000-40142800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr13:40142000-40148800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr13:40142000-40156200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr13:40142000-40156200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr13:40142000-40169400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr13:40142000-40169400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr13:40142200-40142600	Weak transcription	NHDF-Ad	bronchial
39	chr13:40142200-40142600	Weak transcription	Osteobl	bone
40	chr13:40142200-40150000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr13:40142200-40152600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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