Variant report

Variant	rs8078599
Chromosome Location	chr17:37518660-37518661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:37454099..37457029-chr17:37517737..37519979,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11078894	0.84[EUR][1000 genomes]
rs11078895	0.86[EUR][1000 genomes]
rs11078899	0.81[EUR][1000 genomes]
rs11655972	0.89[EUR][1000 genomes]
rs11869259	0.81[ASN][1000 genomes]
rs11871813	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12150047	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12449852	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12938099	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12941418	0.80[EUR][1000 genomes]
rs12950186	0.85[EUR][1000 genomes]
rs1971663	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2302073	0.92[EUR][1000 genomes]
rs2338799	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28482878	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2879258	0.87[EUR][1000 genomes]
rs2879259	0.89[EUR][1000 genomes]
rs28799952	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3744349	0.89[EUR][1000 genomes]
rs4287601	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4516267	0.92[EUR][1000 genomes]
rs4794808	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4795358	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4795367	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57933226	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs582088	0.92[EUR][1000 genomes]
rs582176	0.92[EUR][1000 genomes]
rs584377	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs587880	0.85[EUR][1000 genomes]
rs590051	0.90[EUR][1000 genomes]
rs594794	0.92[EUR][1000 genomes]
rs597069	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs649180	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6503500	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6503504	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs651827	0.91[EUR][1000 genomes]
rs665413	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs667193	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs667239	0.89[EUR][1000 genomes]
rs7208252	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7208487	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7212621	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7215983	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7221117	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7503081	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs801417	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs801418	0.92[EUR][1000 genomes]
rs801427	0.89[EUR][1000 genomes]
rs801429	0.85[EUR][1000 genomes]
rs8067511	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8071300	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8073511	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8073907	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8074276	0.82[EUR][1000 genomes]
rs8074855	0.82[ASN][1000 genomes]
rs9646419	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9890198	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9891892	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9892675	0.82[EUR][1000 genomes]
rs9893735	0.92[EUR][1000 genomes]
rs9899069	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9906612	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9908131	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9909304	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9912212	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9912310	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9944459	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057470	chr17:37135183-37549816	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv543339	chr17:37135183-37549816	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
4	nsv1060126	chr17:37333956-37659189	Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	nsv1057655	chr17:37333956-37732451	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
6	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
7	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
8	nsv908204	chr17:37349655-37682657	Genic enhancers Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv1057057	chr17:37395082-37627025	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	nsv1055612	chr17:37409865-37563236	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1061951	chr17:37442228-37770903	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
12	nsv543341	chr17:37442228-37770903	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
13	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8078599	PGAP3	cis	Thyroid	GTEx
rs8078599	CRKRS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37461400-37522000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:37463800-37528200	Weak transcription	HSMMtube	muscle
3	chr17:37485200-37520800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr17:37489000-37522200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr17:37491600-37520600	Weak transcription	Colon Smooth Muscle	Colon
6	chr17:37492400-37522400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:37496400-37534000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr17:37496600-37520800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:37496800-37522000	Weak transcription	Fetal Stomach	stomach
10	chr17:37498200-37519000	Weak transcription	Placenta	Placenta
11	chr17:37498200-37520200	Weak transcription	Primary B cells from cord blood	blood
12	chr17:37498200-37534200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr17:37498400-37522800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr17:37498600-37520400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr17:37498600-37521000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr17:37498600-37525200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr17:37498600-37529600	Weak transcription	Primary T cells from cord blood	blood
18	chr17:37498600-37532600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr17:37498600-37541200	Weak transcription	Fetal Thymus	thymus
20	chr17:37498600-37543800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr17:37498600-37544000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr17:37498800-37556400	Weak transcription	Thymus	Thymus
23	chr17:37499200-37544000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr17:37509000-37543000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr17:37509600-37522000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr17:37509600-37522000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:37511000-37520600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr17:37512200-37522600	Weak transcription	Gastric	stomach
29	chr17:37514200-37519600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr17:37514800-37556200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr17:37515000-37525800	Weak transcription	Fetal Intestine Small	intestine
32	chr17:37515200-37520000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr17:37515400-37520800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr17:37515400-37555600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr17:37515600-37543200	Weak transcription	Fetal Intestine Large	intestine
36	chr17:37515800-37520400	Weak transcription	Lung	lung
37	chr17:37516000-37519400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr17:37516600-37519800	Weak transcription	Right Atrium	heart
39	chr17:37517200-37520600	Weak transcription	Aorta	Aorta
40	chr17:37517200-37520600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr17:37517200-37520800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr17:37517400-37519800	Weak transcription	Adipose Nuclei	Adipose
43	chr17:37517400-37526000	Weak transcription	Spleen	Spleen
44	chr17:37517600-37519800	Weak transcription	Ovary	ovary
45	chr17:37517600-37520800	Weak transcription	Left Ventricle	heart
46	chr17:37517600-37521000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr17:37517600-37521000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr17:37517600-37521600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr17:37517600-37521600	Weak transcription	Brain Substantia Nigra	brain
50	chr17:37517600-37521600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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