Variant report

Variant	rs4708179
Chromosome Location	chr6:76025603-76025604
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1018471	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10806035	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943241	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs13220419	0.82[GIH][hapmap]
rs171263	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2250989	0.84[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs240375	0.80[CEU][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs240378	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs240379	0.84[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs240380	0.84[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2748252	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808201	0.80[CEU][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs2808203	0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs2842445	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2842446	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2842458	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2842459	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2842461	0.82[GIH][hapmap]
rs2842462	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2842463	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3935857	0.82[CHB][hapmap]
rs4131550	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs4275021	0.91[CEU][hapmap];0.85[CHB][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4295446	0.87[ASN][1000 genomes]
rs4374801	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4412169	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4535511	0.83[ASN][1000 genomes]
rs4541712	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs4568415	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs4708181	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs502900	0.82[GIH][hapmap]
rs6903526	0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6904580	0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs6913979	0.86[CHB][hapmap];0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs6929270	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7451911	0.86[CHB][hapmap]
rs7740648	0.83[ASN][1000 genomes]
rs7743227	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7766441	0.86[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs7771904	0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs7772989	0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs9341514	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs9341515	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9341516	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9343283	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9352202	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352203	0.83[ASN][1000 genomes]
rs9352207	0.82[ASN][1000 genomes]
rs9359122	0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs9443168	0.80[ASN][1000 genomes]
rs9443171	0.86[CHB][hapmap];0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	nsv603764	chr6:75963751-76025603	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv830698	chr6:75968810-76115592	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv1022428	chr6:76023118-76575620	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
9	nsv538312	chr6:76023118-76575620	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4708179	HMGB1P39	cis	Nerve Tibial	GTEx
rs4708179	TMEM30A	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75995400-76027600	Weak transcription	Aorta	Aorta
2	chr6:75995800-76027200	Weak transcription	Fetal Stomach	stomach
3	chr6:76010200-76027400	Weak transcription	Psoas Muscle	Psoas
4	chr6:76010400-76027600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:76016200-76027200	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:76016200-76044400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:76018400-76027600	Weak transcription	Fetal Brain Male	brain
8	chr6:76018800-76026800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:76019200-76026600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:76019200-76026800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:76019200-76027400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:76019600-76027200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:76020600-76027400	Weak transcription	Ovary	ovary
14	chr6:76022200-76028000	Weak transcription	Lung	lung
15	chr6:76022600-76026800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:76022600-76027400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:76022800-76027000	Weak transcription	Fetal Heart	heart
18	chr6:76023400-76027000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:76024400-76027200	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:76024800-76026000	Weak transcription	Fetal Lung	lung
21	chr6:76024800-76026800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:76024800-76027400	Weak transcription	Left Ventricle	heart
23	chr6:76024800-76027400	Weak transcription	Right Ventricle	heart
24	chr6:76024800-76027400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:76024800-76042200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr6:76024800-76047200	Weak transcription	Fetal Muscle Trunk	muscle

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