Variant report

Variant	rs12946510
Chromosome Location	chr17:37912377-37912378
allele	C/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:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:37892523..37898235-chr17:37904182..37913977,22	MCF-7	breast:
2	chr17:37909990..37912890-chr17:37955777..37957738,2	MCF-7	breast:
3	chr17:37771753..37773281-chr17:37910069..37912599,2	K562	blood:
4	chr17:37858985..37861053-chr17:37910558..37912963,2	MCF-7	breast:
5	chr17:37910764..37912781-chr17:37948421..37950091,2	MCF-7	breast:
6	chr17:37885072..37889612-chr17:37908286..37912584,6	MCF-7	breast:
7	chr17:37909095..37912398-chr17:37915882..37918594,4	MCF-7	breast:
8	chr17:37875233..37878023-chr17:37910337..37912992,2	MCF-7	breast:
9	chr17:37907336..37908918-chr17:37910848..37912777,2	MCF-7	breast:
10	chr17:37909648..37914905-chr17:37919305..37927863,11	MCF-7	breast:
11	chr17:37774213..37778029-chr17:37909285..37912435,4	K562	blood:
12	chr17:37908791..37912830-chr17:37925750..37930091,5	K562	blood:
13	chr17:37912256..37913081-chr17:38028636..38029533,2	MCF-7	breast:
14	chr17:37773259..37775797-chr17:37912370..37914095,2	MCF-7	breast:
15	chr17:37789315..37792571-chr17:37910228..37913282,4	K562	blood:
16	chr17:37912341..37914558-chr17:37917986..37920892,4	K562	blood:
17	chr17:37903978..37906952-chr17:37910372..37912419,2	K562	blood:
18	chr17:37912031..37913626-chr17:37916861..37918993,2	MCF-7	breast:
19	chr17:37912122..37914127-chr17:37914525..37916336,2	K562	blood:
20	chr17:37892158..37901988-chr17:37904094..37913282,26	MCF-7	breast:
21	chr17:37790735..37794088-chr17:37909085..37913282,4	K562	blood:
22	chr17:37909376..37912567-chr17:37922952..37926689,4	MCF-7	breast:
23	chr17:37909855..37912536-chr17:38125394..38127110,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000141736	Chromatin interaction
ENSG00000141738	Chromatin interaction
ENSG00000264198	Chromatin interaction
ENSG00000214546	Chromatin interaction
ENSG00000131748	Chromatin interaction
ENSG00000141741	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1008723	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[TSI][hapmap]
rs10445308	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10852936	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.82[TSI][hapmap]
rs11078921	0.80[JPT][hapmap]
rs11078925	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs11078926	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs11078927	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs11557466	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs11557467	0.95[CHB][hapmap];0.97[CHD][hapmap]
rs11658993	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11870965	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs12603332	0.90[CHB][hapmap]
rs12936231	0.95[CHB][hapmap];0.97[CHD][hapmap]
rs12942330	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2290400	0.95[CHB][hapmap];0.91[CHD][hapmap]
rs2305479	0.95[CHB][hapmap];0.94[CHD][hapmap]
rs2305480	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs2313430	0.98[ASN][1000 genomes]
rs2941522	0.99[ASN][1000 genomes]
rs2952140	0.97[ASN][1000 genomes]
rs2952144	0.88[ASN][1000 genomes]
rs3816470	0.95[CHB][hapmap];0.97[CHD][hapmap];0.80[MEX][hapmap]
rs4794820	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4795395	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4795397	0.95[CEU][hapmap]
rs4795400	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs4795405	0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[MEX][hapmap]
rs7216389	0.95[CHB][hapmap];0.94[CHD][hapmap];0.83[MEX][hapmap]
rs7219923	0.91[CHB][hapmap];0.94[CHD][hapmap];0.83[MEX][hapmap]
rs7224129	0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[MEX][hapmap]
rs8069176	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs8076131	0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.87[MEX][hapmap]
rs869402	0.95[CHB][hapmap];0.94[CHD][hapmap];0.83[MEX][hapmap]
rs907091	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.99[ASN][1000 genomes]
rs907092	0.92[CEU][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9303277	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[ASN][1000 genomes]
rs9303280	0.94[CHB][hapmap]
rs9303281	0.95[CHB][hapmap];0.94[CHD][hapmap];0.83[MEX][hapmap]
rs9635726	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs9747973	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9909593	0.88[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv908219	chr17:37880265-37917633	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Inflammatory bowel disease	23128233	GWAS catalog

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12946510	DHRS11	cis	parietal	SCAN
rs12946510	GSDML	Cis_1M	lymphoblastoid	RTeQTL
rs12946510	GSDMB	cis	Whole Blood	GTEx
rs12946510	GSDMB	cis	parietal	SCAN
rs12946510	PIGW	cis	parietal	SCAN
rs12946510	IKZF3	cis	multi-tissue	Pritchard
rs12946510	ORMDL3	cis	lymphoblastoid	seeQTL
rs12946510	ORMDL3	Cis_1M	lymphoblastoid	RTeQTL
rs12946510	ORMDL3	cis	parietal	SCAN
rs12946510	CDC6	cis	cerebellum	SCAN
rs12946510	MED24	cis	parietal	SCAN
rs12946510	CDK12	cis	parietal	SCAN
rs12946510	MED1	cis	cerebellum	SCAN
rs12946510	ORMDL3	cis	multi-tissue	Pritchard
rs12946510	GSDMB	cis	cerebellum	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37909400-37912600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr17:37910800-37912400	Flanking Active TSS	Fetal Thymus	thymus
3	chr17:37910800-37912800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr17:37910800-37913000	Flanking Active TSS	Primary B cells from peripheral blood	blood
5	chr17:37911000-37912400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr17:37911000-37912400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr17:37911000-37912800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr17:37911200-37912400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr17:37911200-37912800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:37911200-37912800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr17:37911200-37912800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr17:37911200-37912800	Enhancers	Fetal Lung	lung
13	chr17:37911200-37912800	Flanking Active TSS	Thymus	Thymus
14	chr17:37911200-37913200	Flanking Active TSS	GM12878-XiMat	blood
15	chr17:37911200-37914000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr17:37911200-37914600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr17:37911200-37914800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr17:37911200-37915000	Enhancers	Primary hematopoietic stem cells	blood
19	chr17:37911400-37912400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr17:37911400-37912400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr17:37911400-37912400	Active TSS	Colonic Mucosa	Colon
22	chr17:37911400-37912800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr17:37911400-37912800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr17:37911400-37913000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:37911400-37913800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr17:37911600-37912400	Bivalent Enhancer	Fetal Muscle Leg	muscle
27	chr17:37911600-37912400	Bivalent Enhancer	Fetal Stomach	stomach
28	chr17:37911600-37912400	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr17:37911600-37912600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
30	chr17:37911600-37912800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr17:37911600-37913000	Enhancers	H1 Cell Line	embryonic stem cell
32	chr17:37911600-37913000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
33	chr17:37911600-37913000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
34	chr17:37911600-37915200	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr17:37911600-37915800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr17:37911800-37912400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
37	chr17:37911800-37913200	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr17:37911800-37913600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr17:37911800-37913600	Weak transcription	HSMM	muscle
40	chr17:37911800-37915400	Enhancers	Duodenum Mucosa	Duodenum
41	chr17:37911800-37918600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr17:37912000-37912400	Enhancers	Dnd41	blood
43	chr17:37912000-37912600	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr17:37912000-37912600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr17:37912000-37912600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr17:37912000-37912800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
47	chr17:37912000-37912800	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr17:37912000-37913200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr17:37912000-37914400	Enhancers	Spleen	Spleen
50	chr17:37912000-37916600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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