Variant report

Variant	rs10484650
Chromosome Location	chr6:53937823-53937824
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10948797	0.94[MEX][hapmap];0.87[AMR][1000 genomes]
rs557018	0.84[MEX][hapmap]
rs73434393	0.84[AMR][1000 genomes]
rs7742036	0.87[AMR][1000 genomes]
rs7753626	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382278	0.89[MEX][hapmap]
rs9382279	0.81[CEU][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9474718	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs961290	0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758055	chr6:53839373-53996093	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv2759431	chr6:53839373-54007349	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv5307	chr6:53874118-53952230	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv603110	chr6:53885918-54103794	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv7901	chr6:53914491-53981080	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv823691	chr6:53918427-53978766	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv885885	chr6:53920024-54046264	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv436993	chr6:53924697-53937823	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
11	nsv436994	chr6:53924697-53937823	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
12	esv34853	chr6:53924697-53977449	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1839673	chr6:53927326-53939724	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
14	esv1835741	chr6:53928649-53939724	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
15	esv1798367	chr6:53929484-53937823	Active TSS Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
16	nsv603117	chr6:53929484-53937823	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
17	nsv603118	chr6:53929484-53939724	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
18	nsv603119	chr6:53929484-53947087	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
19	nsv603120	chr6:53929484-53951857	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv603121	chr6:53929484-53951990	Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
21	nsv603127	chr6:53930541-53937823	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
22	nsv1017633	chr6:53935336-54118476	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10484650	C6orf142	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53928000-53939000	Weak transcription	Left Ventricle	heart
2	chr6:53928600-53939000	Weak transcription	Fetal Heart	heart
3	chr6:53935200-53939400	Weak transcription	Ovary	ovary
4	chr6:53935400-53940600	Weak transcription	Liver	Liver
5	chr6:53935400-53944600	Weak transcription	Right Atrium	heart
6	chr6:53936600-53938000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:53936600-53938000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:53936600-53938000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:53936600-53938000	Enhancers	Right Ventricle	heart
10	chr6:53936600-53938400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr6:53936600-53939400	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr6:53936600-53939600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr6:53936600-53939600	Enhancers	Psoas Muscle	Psoas
14	chr6:53936800-53938000	Enhancers	Adipose Nuclei	Adipose
15	chr6:53936800-53939600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr6:53937000-53938000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:53937000-53939000	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:53937000-53939400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:53937000-53939400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr6:53937000-53939600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr6:53937200-53939200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:53937200-53939200	Weak transcription	HSMM	muscle
23	chr6:53937200-53939600	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr6:53937200-53939600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:53937400-53938000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:53937400-53939600	Enhancers	H1 Cell Line	embryonic stem cell
27	chr6:53937400-53939600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr6:53937800-53938000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:53937800-53938000	Enhancers	H9 Cell Line	embryonic stem cell
30	chr6:53937800-53938000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:53937800-53938000	Enhancers	Fetal Stomach	stomach
32	chr6:53937800-53938400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:53937800-53939200	Weak transcription	HSMMtube	muscle

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