Variant report

Variant	rs12940986
Chromosome Location	chr17:37836581-37836582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:37834714..37837879-chr17:37839609..37842019,3	K562	blood:
2	chr17:37834155..37836946-chr17:37842181..37845040,2	K562	blood:
3	chr17:37833730..37836812-chr17:37841435..37845897,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000141736	Chromatin interaction
ENSG00000161395	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1018246	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1053651	0.86[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.84[TSI][hapmap];0.94[ASN][1000 genomes]
rs10852934	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs11651497	0.88[ASN][1000 genomes]
rs11658786	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11869286	0.88[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12150298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12150603	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12453682	0.85[TSI][hapmap];0.91[YRI][hapmap]
rs14050	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495099	0.89[ASN][1000 genomes]
rs1495100	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495101	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495102	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565920	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565922	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1565923	0.81[CEU][hapmap]
rs1810132	0.81[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.80[MEX][hapmap]
rs1874228	0.87[ASW][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs1877031	0.94[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2247862	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271308	0.82[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.91[ASN][1000 genomes]
rs2271309	0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2313171	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517951	0.83[AMR][1000 genomes]
rs2517952	0.91[ASN][1000 genomes]
rs2517953	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517954	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517955	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517956	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517958	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2517959	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517960	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2934951	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934952	0.90[CEU][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934953	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2934956	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2934971	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap]
rs2941503	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2941504	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2941506	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]
rs2952151	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2952152	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2952155	0.87[CHB][hapmap]
rs2952156	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs33953566	0.88[ASN][1000 genomes]
rs35734596	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3751903	0.89[ASN][1000 genomes]
rs3764352	0.82[ASW][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs3764353	0.88[ASN][1000 genomes]
rs3794712	0.85[ASN][1000 genomes]
rs3817160	0.89[ASN][1000 genomes]
rs407307	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4794817	0.89[ASN][1000 genomes]
rs4795388	0.82[ASN][1000 genomes]
rs4795389	0.87[ASN][1000 genomes]
rs4795390	0.88[ASN][1000 genomes]
rs732083	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732084	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8077172	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8078228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs879606	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs881844	0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs903501	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs903502	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs907087	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907088	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907090	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs907094	0.82[ASW][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs9303274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931992	0.94[ASW][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs9675194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9915323	0.81[ASN][1000 genomes]
rs9972882	0.86[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
8	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
9	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
10	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12940986	GSDMB	cis	cerebellum	SCAN
rs12940986	SLFN14	cis	parietal	SCAN
rs12940986	PGAP3	cis	Thyroid	GTEx
rs12940986	DHRS11	cis	cerebellum	SCAN
rs12940986	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs12940986	SPACA3	cis	parietal	SCAN
rs12940986	PGAP3	cis	Muscle Skeletal	GTEx
rs12940986	PGAP3	cis	Heart Left Ventricle	GTEx
rs12940986	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37827800-37837800	Genic enhancers	Fetal Intestine Small	intestine
2	chr17:37828600-37843200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr17:37828800-37839800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:37829000-37839600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr17:37829000-37839800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr17:37829400-37837400	Enhancers	Primary B cells from cord blood	blood
7	chr17:37829600-37837600	Enhancers	Primary B cells from peripheral blood	blood
8	chr17:37829800-37843600	Weak transcription	NHDF-Ad	bronchial
9	chr17:37830200-37836800	Enhancers	Stomach Mucosa	stomach
10	chr17:37830400-37839400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr17:37830600-37837000	Enhancers	Fetal Thymus	thymus
12	chr17:37830600-37837200	Enhancers	Duodenum Mucosa	Duodenum
13	chr17:37830600-37837400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr17:37830800-37837000	Enhancers	Left Ventricle	heart
15	chr17:37830800-37837600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr17:37830800-37838000	Enhancers	GM12878-XiMat	blood
17	chr17:37831000-37837600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr17:37831200-37837000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr17:37831400-37837000	Enhancers	Right Atrium	heart
20	chr17:37831400-37837600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr17:37831800-37837200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr17:37831800-37837400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr17:37831800-37843400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr17:37831800-37843600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr17:37832000-37839400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr17:37832200-37837200	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr17:37832200-37837400	Enhancers	Primary hematopoietic stem cells	blood
28	chr17:37832200-37844000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr17:37832400-37836800	Genic enhancers	Placenta	Placenta
30	chr17:37832400-37839400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr17:37832600-37837200	Genic enhancers	Fetal Muscle Leg	muscle
32	chr17:37832600-37839600	Weak transcription	Gastric	stomach
33	chr17:37832600-37843200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr17:37832800-37840400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr17:37832800-37843600	Weak transcription	NHEK	skin
36	chr17:37833200-37842400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr17:37833400-37836800	Weak transcription	Colon Smooth Muscle	Colon
38	chr17:37833400-37837600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr17:37833600-37839600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr17:37833600-37843400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:37833600-37843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr17:37833800-37839400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:37833800-37843600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr17:37834000-37836600	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr17:37834400-37838000	Enhancers	Fetal Intestine Large	intestine
46	chr17:37834400-37839400	Weak transcription	Brain Hippocampus Middle	brain
47	chr17:37834400-37839600	Weak transcription	Brain Angular Gyrus	brain
48	chr17:37834400-37843000	Strong transcription	Fetal Stomach	stomach
49	chr17:37834400-37843400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr17:37834400-37843600	Weak transcription	Osteobl	bone

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