Variant report

Variant	rs197917
Chromosome Location	chr17:44999647-44999648
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:44999611-45001014	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:44995313..44999079-chr17:44999263..45002356,3	MCF-7	breast:
2	chr15:44089561..44091456-chr17:44999592..45001929,2	MCF-7	breast:

Variant related genes	Relation type
GOSR2	TF binding region
ENSG00000262633	TF binding region
ENSG00000210709	Chromatin interaction
ENSG00000184716	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1047779	0.99[ASN][1000 genomes]
rs1052504	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1052586	0.98[ASN][1000 genomes]
rs10853085	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10853086	0.88[EUR][1000 genomes]
rs10853087	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11079744	0.84[EUR][1000 genomes]
rs11079745	0.96[ASN][1000 genomes]
rs11652318	0.97[ASN][1000 genomes]
rs11654971	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11655668	0.85[EUR][1000 genomes]
rs11656362	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11658276	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11869840	0.99[ASN][1000 genomes]
rs12601886	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12940071	0.99[ASN][1000 genomes]
rs1618989	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1623402	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662576	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662577	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662594	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662596	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662597	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17608961	0.97[ASN][1000 genomes]
rs1838105	0.88[EUR][1000 genomes]
rs1867237	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs197912	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs197913	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs197915	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs197918	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs197919	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs197922	0.88[EUR][1000 genomes]
rs197923	0.88[EUR][1000 genomes]
rs197925	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs197926	0.97[ASN][1000 genomes]
rs2003538	0.94[ASN][1000 genomes]
rs2003539	0.99[ASN][1000 genomes]
rs2072317	0.83[EUR][1000 genomes]
rs2191033	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2316330	0.97[ASN][1000 genomes]
rs2317997	0.99[ASN][1000 genomes]
rs28553405	0.94[ASN][1000 genomes]
rs2920396	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2920397	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35707546	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3760377	0.97[ASN][1000 genomes]
rs3785888	0.99[ASN][1000 genomes]
rs3809854	0.97[ASN][1000 genomes]
rs3851784	0.97[ASN][1000 genomes]
rs3851785	0.97[ASN][1000 genomes]
rs3851786	0.92[ASN][1000 genomes]
rs3851787	0.94[ASN][1000 genomes]
rs3885731	0.83[EUR][1000 genomes]
rs3890958	0.83[EUR][1000 genomes]
rs4381655	0.97[ASN][1000 genomes]
rs4602097	0.97[ASN][1000 genomes]
rs4968248	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968250	0.96[ASN][1000 genomes]
rs4968285	0.97[ASN][1000 genomes]
rs4968286	0.99[ASN][1000 genomes]
rs4968287	0.96[ASN][1000 genomes]
rs4968288	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4968290	0.87[ASN][1000 genomes]
rs62075889	0.99[ASN][1000 genomes]
rs6504622	0.99[ASN][1000 genomes]
rs7213526	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7225428	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7342957	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs736603	0.99[ASN][1000 genomes]
rs736604	0.99[ASN][1000 genomes]
rs740617	0.99[ASN][1000 genomes]
rs8065527	0.82[EUR][1000 genomes]
rs9889741	0.99[ASN][1000 genomes]
rs9889762	0.97[ASN][1000 genomes]
rs9893713	0.85[ASN][1000 genomes]
rs9898981	0.99[ASN][1000 genomes]
rs9901977	0.85[ASN][1000 genomes]
rs9911967	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv428672	chr17:44872446-45023425	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1067211	chr17:44979111-45057620	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
10	nsv543378	chr17:44979111-45057620	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs197917	GOSR2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:44988200-44999800	Weak transcription	Right Ventricle	heart
2	chr17:44988400-45000000	Weak transcription	Pancreas	Pancrea
3	chr17:44991200-44999800	Weak transcription	Brain Hippocampus Middle	brain
4	chr17:44994200-44999800	Weak transcription	NHLF	lung
5	chr17:44995200-44999800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:44999400-45001200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr17:44999400-45001400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:44999600-44999800	Active TSS	Primary T cells from cord blood	blood
9	chr17:44999600-44999800	Enhancers	Primary hematopoietic stem cells	blood
10	chr17:44999600-44999800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:44999600-45000000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr17:44999600-45000400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr17:44999600-45000600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr17:44999600-45000600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr17:44999600-45000800	Active TSS	Fetal Brain Female	brain
16	chr17:44999600-45001200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr17:44999600-45001200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr17:44999600-45001200	Active TSS	Brain Anterior Caudate	brain
19	chr17:44999600-45001200	Active TSS	Brain Cingulate Gyrus	brain
20	chr17:44999600-45001200	Active TSS	Duodenum Mucosa	Duodenum
21	chr17:44999600-45001200	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr17:44999600-45001400	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr17:44999600-45001400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr17:44999600-45001400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:44999600-45001400	Active TSS	Stomach Smooth Muscle	stomach
26	chr17:44999600-45001800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr17:44999600-45002000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr17:44999600-45002200	Active TSS	HUES64 Cell Line	embryonic stem cell

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