Variant report

Variant	rs665413
Chromosome Location	chr17:37455678-37455679
allele	A/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:
2	chr17:37447109..37449563-chr17:37453918..37456392,2	K562	blood:

Extended variants
information (count: 151 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs10221223	0.81[ASN][1000 genomes]
rs10432030	0.83[ASN][1000 genomes]
rs10432031	0.82[ASN][1000 genomes]
rs10491129	0.87[ASN][1000 genomes]
rs11078894	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11078895	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11078896	0.85[ASN][1000 genomes]
rs11078897	0.85[ASN][1000 genomes]
rs11655972	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11871813	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12150047	0.81[ASN][1000 genomes]
rs12938099	0.81[ASN][1000 genomes]
rs12950186	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1966915	0.85[ASN][1000 genomes]
rs1966916	0.85[ASN][1000 genomes]
rs1971663	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024073	0.87[ASN][1000 genomes]
rs2061338	0.85[ASN][1000 genomes]
rs2061342	0.84[ASN][1000 genomes]
rs2100651	0.83[ASN][1000 genomes]
rs2168785	0.85[ASN][1000 genomes]
rs2302073	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2338755	0.85[ASN][1000 genomes]
rs2338795	0.85[ASN][1000 genomes]
rs2338799	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2338800	0.81[ASN][1000 genomes]
rs2338801	0.80[ASN][1000 genomes]
rs28482878	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2879258	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2879259	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28799952	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33933929	0.84[ASN][1000 genomes]
rs34473775	0.81[ASN][1000 genomes]
rs3744348	0.85[ASN][1000 genomes]
rs3744349	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3964723	0.85[ASN][1000 genomes]
rs4287601	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4325601	0.84[ASN][1000 genomes]
rs4516267	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4794808	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4795355	0.82[ASN][1000 genomes]
rs4795358	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4795367	0.81[ASN][1000 genomes]
rs55689507	0.85[ASN][1000 genomes]
rs57933226	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs582088	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs582176	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs583980	0.83[ASN][1000 genomes]
rs584377	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585961	0.87[ASN][1000 genomes]
rs587343	0.87[ASN][1000 genomes]
rs587880	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs588193	0.85[ASN][1000 genomes]
rs590051	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs593480	0.87[ASN][1000 genomes]
rs594794	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs597069	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs600010	0.85[ASN][1000 genomes]
rs602282	0.84[ASN][1000 genomes]
rs602688	0.87[ASN][1000 genomes]
rs612209	0.90[ASN][1000 genomes]
rs61368704	0.80[ASN][1000 genomes]
rs620686	0.87[ASN][1000 genomes]
rs632202	0.87[ASN][1000 genomes]
rs632606	0.84[ASN][1000 genomes]
rs634365	0.84[ASN][1000 genomes]
rs638201	0.87[ASN][1000 genomes]
rs644173	0.85[ASN][1000 genomes]
rs649180	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs650106	0.87[ASN][1000 genomes]
rs6503500	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6503502	0.81[ASN][1000 genomes]
rs6503504	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs651827	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs667193	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667239	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs677888	0.87[ASN][1000 genomes]
rs679995	0.87[ASN][1000 genomes]
rs683948	0.87[ASN][1000 genomes]
rs7208252	0.85[ASN][1000 genomes]
rs7208487	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7212621	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7215983	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7218484	0.80[ASN][1000 genomes]
rs7218670	0.81[ASN][1000 genomes]
rs7220650	0.81[ASN][1000 genomes]
rs7221117	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7223331	0.81[ASN][1000 genomes]
rs7503081	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs752314	0.85[ASN][1000 genomes]
rs755500	0.85[ASN][1000 genomes]
rs801417	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs801418	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs801419	0.87[ASN][1000 genomes]
rs801420	0.87[ASN][1000 genomes]
rs801426	0.87[ASN][1000 genomes]
rs801427	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs801429	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs801430	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8066704	0.81[ASN][1000 genomes]
rs8067302	0.81[ASN][1000 genomes]
rs8067948	0.81[ASN][1000 genomes]
rs8070695	0.81[ASN][1000 genomes]
rs8071300	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8073511	0.90[ASN][1000 genomes]
rs8073907	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8074855	0.81[ASN][1000 genomes]
rs8078599	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8079355	0.84[ASN][1000 genomes]
rs8079560	0.81[ASN][1000 genomes]
rs8079590	0.85[ASN][1000 genomes]
rs8079662	0.85[ASN][1000 genomes]
rs8081033	0.80[ASN][1000 genomes]
rs8081220	0.87[ASN][1000 genomes]
rs8081338	0.85[ASN][1000 genomes]
rs9646419	0.81[ASN][1000 genomes]
rs9747342	0.87[ASN][1000 genomes]
rs9890198	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9891892	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9893735	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9894586	0.81[ASN][1000 genomes]
rs9894864	0.80[ASN][1000 genomes]
rs9899069	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9903363	0.81[ASN][1000 genomes]
rs9904334	0.87[ASN][1000 genomes]
rs9905617	0.81[ASN][1000 genomes]
rs9906612	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9908131	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9908760	0.81[ASN][1000 genomes]
rs9909064	0.81[ASN][1000 genomes]
rs9909304	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9912212	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9912310	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9913320	0.85[ASN][1000 genomes]
rs9944411	0.81[ASN][1000 genomes]
rs9944459	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv833441	chr17:37320807-37476796	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv1061084	chr17:37333956-37501598	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv510709	chr17:37438419-37508395	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	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
15	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs665413	PGAP3	cis	Thyroid	GTEx
rs665413	CRKRS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37408000-37463000	Weak transcription	Small Intestine	intestine
2	chr17:37409800-37464000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:37417400-37458600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr17:37417600-37460800	Weak transcription	Fetal Brain Male	brain
5	chr17:37425000-37473000	Weak transcription	Pancreas	Pancrea
6	chr17:37426600-37460800	Weak transcription	Colonic Mucosa	Colon
7	chr17:37426800-37468600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr17:37430800-37462600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:37431200-37462600	Weak transcription	Colon Smooth Muscle	Colon
10	chr17:37431400-37473400	Weak transcription	Esophagus	oesophagus
11	chr17:37433800-37457000	Weak transcription	GM12878-XiMat	blood
12	chr17:37435600-37469400	Weak transcription	Gastric	stomach
13	chr17:37436000-37496200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr17:37436800-37497800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr17:37437800-37462400	Weak transcription	Brain Anterior Caudate	brain
16	chr17:37438400-37461800	Weak transcription	A549	lung
17	chr17:37438600-37456600	Weak transcription	HSMM	muscle
18	chr17:37438800-37463000	Weak transcription	NHDF-Ad	bronchial
19	chr17:37439000-37462800	Weak transcription	NH-A	brain
20	chr17:37439200-37457200	Weak transcription	K562	blood
21	chr17:37439200-37462600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr17:37439200-37462800	Weak transcription	Fetal Heart	heart
23	chr17:37444000-37478400	Weak transcription	Psoas Muscle	Psoas
24	chr17:37444600-37462600	Strong transcription	Fetal Intestine Small	intestine
25	chr17:37446000-37459400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:37446800-37459600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr17:37447400-37457800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr17:37448000-37456000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr17:37448200-37457800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr17:37448200-37458800	Weak transcription	HUVEC	blood vessel
31	chr17:37448400-37458000	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr17:37448400-37461800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr17:37449200-37461000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr17:37449600-37456400	Strong transcription	Fetal Brain Female	brain
35	chr17:37449800-37457600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr17:37450000-37457400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr17:37450800-37456800	Weak transcription	NHEK	skin
38	chr17:37450800-37460200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr17:37451000-37458000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr17:37451000-37459400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr17:37451200-37457400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr17:37451200-37458000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr17:37451400-37456800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr17:37451400-37457400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr17:37451400-37457600	Strong transcription	Fetal Lung	lung
46	chr17:37451400-37460200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr17:37452000-37458600	Weak transcription	Stomach Mucosa	stomach
48	chr17:37452200-37457600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:37452400-37457400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr17:37452600-37457600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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