Variant report

Variant	rs6755776
Chromosome Location	chr2:152897670-152897671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10930888	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930892	0.89[CEU][hapmap]
rs12471157	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12474775	0.80[ASN][1000 genomes]
rs16830598	0.90[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap]
rs16830616	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes]
rs1949521	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes]
rs2139417	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2680982	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2881059	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs35478891	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3845845	0.90[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs4146376	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4664075	0.89[EUR][1000 genomes]
rs4664076	0.82[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.85[MEX][hapmap]
rs4664513	0.81[CHB][hapmap]
rs4664524	0.80[ASN][1000 genomes]
rs58147624	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs58248711	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58402146	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58761979	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61156093	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6433726	0.81[CHB][hapmap]
rs6433777	0.82[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap]
rs6721518	0.81[CHB][hapmap]
rs6728019	0.81[CHB][hapmap]
rs7604835	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs7607695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9917162	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9917211	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9917218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv875290	chr2:152803129-152920126	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6755776	C11orf17	trans	cerebellum	SCAN
rs6755776	TNFAIP6	cis	parietal	SCAN
rs6755776	STAM2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152890000-152904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:152893400-152898000	Enhancers	Fetal Stomach	stomach
3	chr2:152894400-152899400	Weak transcription	Fetal Thymus	thymus
4	chr2:152894400-152899600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:152894600-152898600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:152894600-152898800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:152895000-152899400	Weak transcription	Fetal Brain Female	brain
8	chr2:152895400-152897800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:152895400-152898400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:152895400-152898400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:152895400-152898400	Weak transcription	Placenta	Placenta
12	chr2:152895400-152898600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:152895400-152899400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:152895400-152899400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:152895400-152900600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:152895400-152903200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:152895600-152898600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:152895600-152898800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:152895600-152899000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:152895600-152899200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:152895600-152899200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:152895600-152899800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr2:152895800-152899400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr2:152896400-152900000	Weak transcription	Fetal Brain Male	brain
25	chr2:152897200-152897800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:152897200-152897800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:152897400-152899200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:152897400-152900000	Enhancers	Fetal Muscle Leg	muscle
29	chr2:152897400-152900600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:152897600-152898000	Weak transcription	Fetal Lung	lung
31	chr2:152897600-152900200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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