Variant report

Variant	rs2941506
Chromosome Location	chr17:37833035-37833036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:37827266..37833048-chr17:37842420..37846685,6	MCF-7	breast:
2	chr17:37831185..37834082-chr17:37834378..37836489,3	MCF-7	breast:
3	chr17:37832659..37835422-chr17:37879679..37882174,3	K562	blood:
4	chr17:37829760..37835390-chr17:37853762..37858979,8	MCF-7	breast:
5	chr17:37806036..37809512-chr17:37829090..37833058,4	K562	blood:
6	chr17:37832364..37833972-chr17:37842074..37844031,2	K562	blood:

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

Extended variants
information (count: 89 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1018246	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1053651	0.85[CHB][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs10852934	0.87[ASN][1000 genomes]
rs11651497	0.87[ASN][1000 genomes]
rs11658786	0.92[ASN][1000 genomes]
rs11869286	0.85[CHB][hapmap];0.83[JPT][hapmap];0.95[ASN][1000 genomes]
rs12150298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12150603	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12940986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs14050	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1476278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495099	0.88[ASN][1000 genomes]
rs1495100	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495101	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495102	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565920	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565922	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565923	0.81[CEU][hapmap]
rs1810132	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs1874228	0.86[ASN][1000 genomes]
rs1877031	0.85[CHB][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs2247862	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271308	0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs2271309	0.88[ASN][1000 genomes]
rs2313171	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517952	0.91[ASN][1000 genomes]
rs2517953	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2517954	0.86[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517955	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517956	0.85[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2517957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517958	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517959	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517960	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2934951	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934952	0.90[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934953	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934956	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934971	0.80[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2941503	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941504	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952151	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2952152	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2952155	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2952156	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs33953566	0.87[ASN][1000 genomes]
rs35734596	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[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	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732084	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077172	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879606	0.87[ASN][1000 genomes]
rs881844	0.81[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs903501	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs903502	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907087	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907088	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907089	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907090	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907094	0.87[ASN][1000 genomes]
rs9303274	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs931992	0.84[JPT][hapmap]
rs9675194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915323	0.80[ASN][1000 genomes]
rs9972882	0.85[CHB][hapmap];0.84[JPT][hapmap];0.94[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	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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	esv1848656	chr17:37830900-37834998	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2941506	PGAP3	cis	Heart Left Ventricle	GTEx
rs2941506	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs2941506	PGAP3	cis	Muscle Skeletal	GTEx
rs2941506	PGAP3	cis	Skin Sun Exposed Lower leg	GTEx
rs2941506	PGAP3	cis	Thyroid	GTEx
rs2941506	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37824800-37833200	Enhancers	Fetal Heart	heart
2	chr17:37827800-37837800	Genic enhancers	Fetal Intestine Small	intestine
3	chr17:37828400-37834000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr17:37828400-37834200	Weak transcription	Fetal Kidney	kidney
5	chr17:37828600-37833200	Weak transcription	Brain Anterior Caudate	brain
6	chr17:37828600-37834200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr17:37828600-37836000	Weak transcription	Ovary	ovary
8	chr17:37828600-37843200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr17:37828800-37835400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr17:37828800-37839800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr17:37829000-37839600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr17:37829000-37839800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr17:37829400-37834000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:37829400-37837400	Enhancers	Primary B cells from cord blood	blood
15	chr17:37829600-37835600	Weak transcription	Brain Germinal Matrix	brain
16	chr17:37829600-37837600	Enhancers	Primary B cells from peripheral blood	blood
17	chr17:37829800-37833800	Enhancers	Right Ventricle	heart
18	chr17:37829800-37834000	Strong transcription	Fetal Stomach	stomach
19	chr17:37829800-37835000	Enhancers	Placenta Amnion	Placenta Amnion
20	chr17:37829800-37843600	Weak transcription	NHDF-Ad	bronchial
21	chr17:37830200-37836800	Enhancers	Stomach Mucosa	stomach
22	chr17:37830400-37834200	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr17:37830400-37839400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr17:37830600-37833600	Enhancers	Esophagus	oesophagus
25	chr17:37830600-37834600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr17:37830600-37835200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr17:37830600-37837000	Enhancers	Fetal Thymus	thymus
28	chr17:37830600-37837200	Enhancers	Duodenum Mucosa	Duodenum
29	chr17:37830600-37837400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr17:37830800-37835600	Enhancers	Primary T cells fromperipheralblood	blood
31	chr17:37830800-37837000	Enhancers	Left Ventricle	heart
32	chr17:37830800-37837600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr17:37830800-37838000	Enhancers	GM12878-XiMat	blood
34	chr17:37831000-37835200	Enhancers	A549	lung
35	chr17:37831000-37836000	Enhancers	HSMMtube	muscle
36	chr17:37831000-37836400	Enhancers	Psoas Muscle	Psoas
37	chr17:37831000-37837600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr17:37831200-37833200	Enhancers	Stomach Smooth Muscle	stomach
39	chr17:37831200-37833600	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr17:37831200-37835800	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr17:37831200-37837000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr17:37831400-37833800	Weak transcription	Small Intestine	intestine
43	chr17:37831400-37835600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr17:37831400-37837000	Enhancers	Right Atrium	heart
45	chr17:37831400-37837600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr17:37831600-37833400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr17:37831600-37834000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr17:37831600-37835600	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr17:37831600-37835800	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr17:37831600-37836400	Enhancers	Colonic Mucosa	Colon

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