Variant report

Variant	rs9972882
Chromosome Location	chr17:37807698-37807699
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:37806444..37808313-chr17:37808562..37810244,2	K562	blood:
2	chr17:37806774..37809121-chr17:37895420..37897002,2	MCF-7	breast:
3	chr17:37792000..37794042-chr17:37806624..37808948,2	MCF-7	breast:
4	chr17:37806164..37807865-chr17:37817828..37819682,2	MCF-7	breast:
5	chr17:37806279..37807957-chr17:37817089..37818610,2	K562	blood:
6	chr17:37777435..37780800-chr17:37803920..37808668,4	K562	blood:
7	chr17:37806514..37808677-chr17:37883983..37886085,2	K562	blood:

Variant related genes	Relation type
ENSG00000131748	Chromatin interaction
ENSG00000141736	Chromatin interaction
ENSG00000141738	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1018246	0.94[ASN][1000 genomes]
rs1053651	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10852934	0.89[ASW][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11651497	0.91[ASN][1000 genomes]
rs11654018	0.80[CEU][hapmap]
rs11658678	0.85[CEU][hapmap]
rs11658786	0.97[ASN][1000 genomes]
rs11869286	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.99[ASN][1000 genomes]
rs12150298	0.86[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs12150603	0.86[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs12450559	0.80[CEU][hapmap]
rs12453682	0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs12940986	0.86[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs14050	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.94[ASN][1000 genomes]
rs1476278	0.86[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs1495099	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1495100	0.94[ASN][1000 genomes]
rs1495101	0.94[ASN][1000 genomes]
rs1495102	0.94[ASN][1000 genomes]
rs1565920	0.94[ASN][1000 genomes]
rs1565922	0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.94[ASN][1000 genomes]
rs1810132	0.83[GIH][hapmap];0.81[TSI][hapmap]
rs1874228	0.84[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs1877031	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.99[ASN][1000 genomes]
rs2247862	0.83[ASW][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.94[ASN][1000 genomes]
rs2271308	0.90[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271309	0.87[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs2303316	0.80[CEU][hapmap]
rs2313171	0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2517952	0.85[ASN][1000 genomes]
rs2517953	0.88[ASN][1000 genomes]
rs2517954	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2517955	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2517956	0.83[ASW][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs2517957	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2517958	0.86[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2517959	0.87[ASN][1000 genomes]
rs2517960	0.85[ASN][1000 genomes]
rs2934951	0.94[ASN][1000 genomes]
rs2934952	0.94[ASN][1000 genomes]
rs2934953	0.81[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs2934956	0.94[ASN][1000 genomes]
rs2934971	0.83[GIH][hapmap];0.87[TSI][hapmap]
rs2941503	0.91[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.94[ASN][1000 genomes]
rs2941504	0.83[ASW][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.95[ASN][1000 genomes]
rs2941505	0.86[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs2941506	0.85[CHB][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs2952151	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.94[ASN][1000 genomes]
rs2952152	0.93[ASN][1000 genomes]
rs33953566	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35734596	0.86[ASN][1000 genomes]
rs3751903	0.92[ASN][1000 genomes]
rs3764351	0.82[ASN][1000 genomes]
rs3764352	0.87[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs3764353	0.91[ASN][1000 genomes]
rs3794712	0.88[ASN][1000 genomes]
rs3817160	0.92[ASN][1000 genomes]
rs407307	0.92[ASN][1000 genomes]
rs4239222	0.80[CEU][hapmap]
rs4794814	0.80[CEU][hapmap]
rs4794817	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4795388	0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs4795389	0.90[ASN][1000 genomes]
rs4795390	0.91[ASN][1000 genomes]
rs732083	0.94[ASN][1000 genomes]
rs732084	0.94[ASN][1000 genomes]
rs7503069	0.80[CEU][hapmap]
rs7503705	0.80[CEU][hapmap]
rs8065963	0.80[CEU][hapmap]
rs8077172	0.94[ASN][1000 genomes]
rs8078228	0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs879606	0.89[ASW][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs881844	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs903501	0.83[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap];0.94[ASN][1000 genomes]
rs903502	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.94[ASN][1000 genomes]
rs907087	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.94[ASN][1000 genomes]
rs907088	0.94[ASN][1000 genomes]
rs907089	0.86[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs907090	0.94[ASN][1000 genomes]
rs907094	0.87[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs9303274	0.86[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs931992	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap]
rs9675194	0.86[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs9915323	0.90[CEU][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9972882	SPACA3	cis	parietal	SCAN
rs9972882	PGAP3	cis	Thyroid	GTEx
rs9972882	PGAP3	cis	cerebellum	SCAN
rs9972882	PGAP3	cis	Heart Left Ventricle	GTEx
rs9972882	PGAP3	cis	Stomach	GTEx
rs9972882	CRKRS	Cis_1M	lymphoblastoid	RTeQTL
rs9972882	DHRS11	cis	parietal	SCAN
rs9972882	SLFN14	cis	parietal	SCAN
rs9972882	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs9972882	DHRS11	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37795000-37814000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr17:37795000-37823800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr17:37795200-37814000	Weak transcription	Aorta	Aorta
4	chr17:37795200-37814600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr17:37795400-37818000	Weak transcription	Fetal Kidney	kidney
6	chr17:37795600-37808600	Weak transcription	Fetal Lung	lung
7	chr17:37796200-37808000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr17:37796200-37808600	Strong transcription	Fetal Stomach	stomach
9	chr17:37796400-37810000	Weak transcription	Colon Smooth Muscle	Colon
10	chr17:37796400-37810800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr17:37796600-37809800	Weak transcription	Dnd41	blood
12	chr17:37797000-37808800	Weak transcription	Brain Germinal Matrix	brain
13	chr17:37797200-37808000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr17:37798200-37813800	Weak transcription	GM12878-XiMat	blood
15	chr17:37798800-37808200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:37798800-37808800	Weak transcription	Ovary	ovary
17	chr17:37798800-37810400	Weak transcription	Fetal Thymus	thymus
18	chr17:37799800-37808200	Weak transcription	Colonic Mucosa	Colon
19	chr17:37799800-37809400	Weak transcription	Liver	Liver
20	chr17:37799800-37812400	Weak transcription	Psoas Muscle	Psoas
21	chr17:37799800-37819600	Weak transcription	Osteobl	bone
22	chr17:37800000-37809400	Weak transcription	Adipose Nuclei	Adipose
23	chr17:37800000-37809400	Weak transcription	Esophagus	oesophagus
24	chr17:37800000-37809800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr17:37800000-37810000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr17:37800000-37812800	Weak transcription	NHLF	lung
27	chr17:37800000-37814000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr17:37800000-37815200	Weak transcription	HUVEC	blood vessel
29	chr17:37800000-37818600	Weak transcription	Hela-S3	cervix
30	chr17:37800000-37820000	Weak transcription	NH-A	brain
31	chr17:37800200-37809200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr17:37800200-37810000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr17:37800200-37810600	Enhancers	Fetal Brain Male	brain
34	chr17:37800200-37810600	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr17:37800200-37816800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr17:37800400-37808000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr17:37800400-37808400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr17:37800400-37814000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr17:37800600-37808200	Weak transcription	Brain Angular Gyrus	brain
40	chr17:37800600-37816200	Weak transcription	NHEK	skin
41	chr17:37800800-37808200	Weak transcription	Brain Anterior Caudate	brain
42	chr17:37800800-37808200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr17:37800800-37810000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr17:37801000-37814600	Weak transcription	Primary B cells from cord blood	blood
45	chr17:37801200-37809800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr17:37801400-37809400	Weak transcription	Right Atrium	heart
47	chr17:37801600-37808200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr17:37801600-37808200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:37801600-37808200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr17:37801600-37808800	Weak transcription	Fetal Muscle Trunk	muscle

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