Variant report

Variant	rs331068
Chromosome Location	chr5:127749298-127749299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11741832	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11742635	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs13155917	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs13159256	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs13164781	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs13175872	0.86[CHB][hapmap]
rs13179424	0.82[ASN][1000 genomes]
rs13180243	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs13181926	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs13182859	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[ASN][1000 genomes]
rs13190457	0.86[ASN][1000 genomes]
rs1561004	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[ASN][1000 genomes]
rs17677069	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[ASN][1000 genomes]
rs17677346	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs17677555	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs331071	0.86[JPT][hapmap]
rs34806389	0.86[ASN][1000 genomes]
rs3805646	0.88[JPT][hapmap]
rs3805651	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[ASN][1000 genomes]
rs3805653	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs3828661	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[ASN][1000 genomes]
rs4836375	0.88[CHB][hapmap]
rs62391604	0.86[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	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv599698	chr5:127744825-127850855	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
3	nsv1015650	chr5:127745955-127866566	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
4	esv2763497	chr5:127745955-127882468	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs331068	CSF2	cis	cerebellum	SCAN
rs331068	CHSY3	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127725800-127765600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:127739200-127789000	Weak transcription	Left Ventricle	heart
3	chr5:127739400-127759800	Weak transcription	Fetal Lung	lung
4	chr5:127740800-127759600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:127741000-127751400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:127743000-127760400	Weak transcription	A549	lung
7	chr5:127743400-127771800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:127744400-127762200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:127745200-127773800	Weak transcription	Right Ventricle	heart
10	chr5:127745400-127756600	Weak transcription	Fetal Kidney	kidney
11	chr5:127746000-127754600	Weak transcription	Hela-S3	cervix
12	chr5:127746000-127777600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:127746200-127750200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:127746400-127749800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:127747000-127749600	Weak transcription	NHEK	skin
16	chr5:127747400-127750000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:127747400-127751600	Weak transcription	Fetal Stomach	stomach
18	chr5:127747400-127756600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr5:127747400-127758600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:127747400-127759200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:127747400-127759200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:127747400-127772400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:127747600-127749800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:127747600-127756600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:127747600-127784400	Weak transcription	Placenta	Placenta
26	chr5:127748200-127750200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:127748400-127749400	Enhancers	Fetal Heart	heart
28	chr5:127748400-127749800	Enhancers	HUVEC	blood vessel
29	chr5:127748800-127749800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr5:127748800-127772400	Weak transcription	NH-A	brain
31	chr5:127749200-127749600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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