Variant report

Variant	rs4616955
Chromosome Location	chr6:76089446-76089447
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16886446	0.80[GIH][hapmap];1.00[JPT][hapmap]
rs16886475	0.81[CHB][hapmap]
rs2748254	0.85[JPT][hapmap];0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
7	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
8	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
9	nsv1032245	chr6:76045537-76545703	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
10	nsv538313	chr6:76045537-76545703	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4616955	COL9A3	trans	lymphoblastoid	seeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76085200-76091600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr6:76085200-76092000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:76086200-76091800	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:76086200-76091800	Weak transcription	NHLF	lung
5	chr6:76086400-76091600	Weak transcription	Fetal Lung	lung
6	chr6:76086600-76091800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr6:76086800-76091600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr6:76086800-76092000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:76087200-76091600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:76087400-76090200	Weak transcription	NHDF-Ad	bronchial
11	chr6:76087400-76091600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:76087400-76091800	Weak transcription	Aorta	Aorta
13	chr6:76087400-76100800	Weak transcription	Psoas Muscle	Psoas
14	chr6:76087800-76091800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:76088000-76091600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:76088200-76091400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:76088200-76091600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:76088200-76091600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:76088200-76092000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:76088400-76089600	Weak transcription	A549	lung
21	chr6:76088400-76091800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:76088400-76092000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:76088400-76092000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:76088400-76105800	Weak transcription	Placenta	Placenta
25	chr6:76088600-76091200	Weak transcription	Fetal Heart	heart
26	chr6:76088600-76091800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:76088600-76091800	Weak transcription	Right Ventricle	heart
28	chr6:76089000-76089600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:76089000-76089600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr6:76089200-76089600	Enhancers	Left Ventricle	heart
31	chr6:76089200-76089800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:76089400-76091800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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