Variant report

Variant	rs2934956
Chromosome Location	chr17:37830447-37830448
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:37827266..37833048-chr17:37842420..37846685,6	MCF-7	breast:
2	chr17:37829376..37831831-chr17:37883917..37885766,2	K562	blood:
3	chr17:37814743..37816987-chr17:37828595..37830595,2	MCF-7	breast:
4	chr17:37793727..37796192-chr17:37829753..37832726,2	MCF-7	breast:
5	chr17:37827137..37831259-chr17:37846824..37848519,3	K562	blood:
6	chr17:37829760..37835390-chr17:37853762..37858979,8	MCF-7	breast:
7	chr17:37827978..37830738-chr17:37885762..37888440,2	MCF-7	breast:
8	chr17:37806036..37809512-chr17:37829090..37833058,4	K562	blood:
9	chr17:37828636..37830492-chr17:37908075..37910484,2	K562	blood:
10	chr17:37829190..37831806-chr17:37886312..37888416,2	MCF-7	breast:
11	chr17:37829895..37831934-chr17:37839264..37841541,2	MCF-7	breast:
12	chr17:37830304..37832769-chr17:37860083..37864558,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000161395	Chromatin interaction
ENSG00000141741	Chromatin interaction
ENSG00000131748	Chromatin interaction
ENSG00000141736	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1018246	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1053651	0.94[ASN][1000 genomes]
rs10852934	0.87[ASN][1000 genomes]
rs11651497	0.87[ASN][1000 genomes]
rs11658786	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11869286	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12150298	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12150603	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12940986	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs14050	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1476278	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1495099	0.88[ASN][1000 genomes]
rs1495100	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495101	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495102	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565920	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1565922	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1874228	0.86[ASN][1000 genomes]
rs1877031	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2247862	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271308	0.92[ASN][1000 genomes]
rs2271309	0.88[ASN][1000 genomes]
rs2313171	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517951	0.80[AMR][1000 genomes]
rs2517952	0.89[ASN][1000 genomes]
rs2517953	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517954	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2517955	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2517956	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2517957	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517958	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517959	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2517960	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2934951	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934952	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934953	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941503	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941504	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941505	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941506	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2952151	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2952152	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33953566	0.87[ASN][1000 genomes]
rs35734596	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3751903	0.88[ASN][1000 genomes]
rs3764352	0.87[ASN][1000 genomes]
rs3764353	0.87[ASN][1000 genomes]
rs3794712	0.84[ASN][1000 genomes]
rs3817160	0.88[ASN][1000 genomes]
rs407307	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4794817	0.88[ASN][1000 genomes]
rs4795388	0.82[ASN][1000 genomes]
rs4795389	0.86[ASN][1000 genomes]
rs4795390	0.87[ASN][1000 genomes]
rs732083	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732084	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8077172	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8078228	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs879606	0.87[ASN][1000 genomes]
rs881844	0.91[ASN][1000 genomes]
rs903501	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs903502	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907087	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907088	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907089	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907090	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907094	0.87[ASN][1000 genomes]
rs9303274	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9675194	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9915323	0.80[ASN][1000 genomes]
rs9972882	0.94[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	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
2	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
3	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv908205	chr17:37709422-37830900	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
8	nsv457738	chr17:37770005-37831035	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv574991	chr17:37770005-37831035	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers 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	18 gene(s)	inside rSNPs	diseases
10	nsv516757	chr17:37781849-37834541	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
11	esv1792029	chr17:37797757-37886460	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv908213	chr17:37807698-37839493	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
13	nsv528093	chr17:37814080-37866005	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	nsv908214	chr17:37814224-37861833	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv908215	chr17:37818561-37834541	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2934956	PGAP3	cis	Skin Sun Exposed Lower leg	GTEx
rs2934956	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs2934956	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs2934956	PGAP3	cis	Thyroid	GTEx
rs2934956	PGAP3	cis	Heart Left Ventricle	GTEx
rs2934956	PGAP3	cis	Stomach	GTEx
rs2934956	PGAP3	cis	Muscle Skeletal	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37824600-37831000	Weak transcription	Gastric	stomach
2	chr17:37824800-37833200	Enhancers	Fetal Heart	heart
3	chr17:37825200-37831200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr17:37825200-37832600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr17:37825200-37833000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr17:37825800-37833000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:37826400-37833000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr17:37826800-37830800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr17:37827600-37832800	Enhancers	Fetal Intestine Large	intestine
10	chr17:37827800-37837800	Genic enhancers	Fetal Intestine Small	intestine
11	chr17:37828400-37832000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr17:37828400-37832200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr17:37828400-37832400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr17:37828400-37832600	Weak transcription	Fetal Brain Female	brain
15	chr17:37828400-37834000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr17:37828400-37834200	Weak transcription	Fetal Kidney	kidney
17	chr17:37828600-37830600	Weak transcription	Fetal Thymus	thymus
18	chr17:37828600-37830800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr17:37828600-37830800	Weak transcription	Right Atrium	heart
20	chr17:37828600-37831000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr17:37828600-37831000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr17:37828600-37831400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr17:37828600-37831400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr17:37828600-37831400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr17:37828600-37831600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr17:37828600-37831600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr17:37828600-37831800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr17:37828600-37831800	Weak transcription	Adipose Nuclei	Adipose
29	chr17:37828600-37832000	Weak transcription	Liver	Liver
30	chr17:37828600-37832200	Weak transcription	Brain Angular Gyrus	brain
31	chr17:37828600-37832200	Weak transcription	Brain Substantia Nigra	brain
32	chr17:37828600-37833000	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr17:37828600-37833200	Weak transcription	Brain Anterior Caudate	brain
34	chr17:37828600-37834200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr17:37828600-37836000	Weak transcription	Ovary	ovary
36	chr17:37828600-37843200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr17:37828800-37830600	Weak transcription	Fetal Muscle Leg	muscle
38	chr17:37828800-37831000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr17:37828800-37831200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr17:37828800-37831200	Weak transcription	Brain Hippocampus Middle	brain
41	chr17:37828800-37831200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr17:37828800-37831600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr17:37828800-37831800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr17:37828800-37831800	Weak transcription	Lung	lung
45	chr17:37828800-37832000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr17:37828800-37832600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr17:37828800-37835400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr17:37828800-37839800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr17:37829000-37830600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr17:37829000-37830600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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