Variant report

Variant	rs7215889
Chromosome Location	chr17:37407762-37407763
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	chr17:37407020..37409663-chr17:37431411..37433036,2	K562	blood:
2	chr17:37402739..37404636-chr17:37405681..37408393,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10221223	0.82[EUR][1000 genomes]
rs10432030	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10432031	0.83[EUR][1000 genomes]
rs10491129	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11078893	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11078896	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11078897	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1966915	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1966916	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2024073	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2061338	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2061342	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2100651	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2168785	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2338755	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2338756	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2338795	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs33933929	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34473775	0.82[EUR][1000 genomes]
rs3744348	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3964723	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4325601	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4375688	0.81[ASN][1000 genomes]
rs4795355	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55689507	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs583980	0.82[EUR][1000 genomes]
rs585961	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs587343	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs588193	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs593480	0.82[ASN][1000 genomes]
rs600010	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs602282	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs602688	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs612209	0.81[EUR][1000 genomes]
rs620686	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62074994	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs632202	0.82[ASN][1000 genomes]
rs634365	0.83[EUR][1000 genomes]
rs638201	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs644173	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs650106	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6503503	0.80[EUR][1000 genomes]
rs677888	0.82[ASN][1000 genomes]
rs679995	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs683948	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7359658	0.80[EUR][1000 genomes]
rs752314	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs755500	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs801419	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs801420	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs801426	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8066704	0.83[EUR][1000 genomes]
rs8067948	0.83[EUR][1000 genomes]
rs8070695	0.81[EUR][1000 genomes]
rs8076494	0.80[EUR][1000 genomes]
rs8079590	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8079662	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8081220	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8081338	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9747342	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9894500	0.80[EUR][1000 genomes]
rs9894864	0.80[EUR][1000 genomes]
rs9898170	0.80[EUR][1000 genomes]
rs9904334	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9908760	0.80[EUR][1000 genomes]
rs9913320	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9944411	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7215889	PGAP3	cis	Thyroid	GTEx
rs7215889	CRKRS	Cis_1M	lymphoblastoid	RTeQTL
rs7215889	PGAP3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37395000-37413000	Weak transcription	HSMMtube	muscle
2	chr17:37395000-37414600	Weak transcription	Psoas Muscle	Psoas
3	chr17:37395200-37409000	Weak transcription	Brain Anterior Caudate	brain
4	chr17:37395200-37409200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr17:37395200-37417000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr17:37396000-37409200	Weak transcription	Pancreas	Pancrea
7	chr17:37396400-37410200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:37396400-37416400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr17:37400800-37410600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:37401000-37407800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr17:37401000-37408000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:37401000-37408000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr17:37401000-37408000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr17:37401000-37408200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr17:37401000-37408400	Weak transcription	Fetal Intestine Large	intestine
16	chr17:37401000-37408600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr17:37401000-37409000	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr17:37401000-37409000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr17:37401000-37409200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr17:37401000-37409200	Weak transcription	Brain Hippocampus Middle	brain
21	chr17:37401000-37409200	Weak transcription	Brain Substantia Nigra	brain
22	chr17:37401000-37409200	Weak transcription	Right Ventricle	heart
23	chr17:37401000-37409400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr17:37401000-37413400	Weak transcription	HSMM	muscle
25	chr17:37401000-37414200	Weak transcription	Fetal Brain Male	brain
26	chr17:37401000-37414200	Weak transcription	NHDF-Ad	bronchial
27	chr17:37401000-37426000	Weak transcription	NHLF	lung
28	chr17:37401000-37433000	Weak transcription	Fetal Heart	heart
29	chr17:37401000-37437000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr17:37401200-37408000	Weak transcription	Fetal Lung	lung
31	chr17:37401200-37408200	Weak transcription	Primary T cells from cord blood	blood
32	chr17:37401200-37408200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr17:37401200-37408400	Weak transcription	Fetal Brain Female	brain
34	chr17:37401200-37409000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr17:37401200-37409000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr17:37401200-37409000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr17:37401200-37409200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr17:37401200-37409200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr17:37401200-37409200	Weak transcription	Fetal Thymus	thymus
40	chr17:37401200-37409200	Weak transcription	Lung	lung
41	chr17:37401200-37409200	Weak transcription	Ovary	ovary
42	chr17:37401200-37409200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr17:37401200-37409200	Weak transcription	Spleen	Spleen
44	chr17:37401200-37409200	Weak transcription	Dnd41	blood
45	chr17:37401200-37409200	Weak transcription	GM12878-XiMat	blood
46	chr17:37401200-37412800	Weak transcription	Colon Smooth Muscle	Colon
47	chr17:37401200-37414000	Weak transcription	Fetal Kidney	kidney
48	chr17:37401200-37414400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr17:37401400-37408000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr17:37401400-37408000	Weak transcription	Primary B cells from cord blood	blood

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