Variant report

Variant	rs12221497
Chromosome Location	chr11:47280653-47280654
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:47280600-47280750	HCM	heart:	n/a	n/a
2	RAD21	chr11:47280643-47281615	SK-N-SH	brain:	n/a	n/a
3	SMC3	chr11:47280556-47281491	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr11:47278588-47281976	A549	lung:	n/a	chr11:47278969-47278982
5	RAD21	chr11:47280649-47281558	A549	lung:	n/a	n/a
6	HCFC1	chr11:47278486-47281950	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr11:47280651-47281550	HCT-116	colon:	n/a	n/a
8	POLR2A	chr11:47280621-47281259	Hela-S3	cervix:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47197631..47199665-chr11:47279516..47282212,2	K562	blood:
2	chr11:47206745..47208837-chr11:47280102..47282885,2	K562	blood:
3	chr11:47196892..47202921-chr11:47278417..47285951,9	MCF-7	breast:
4	chr11:47205835..47208468-chr11:47280225..47282817,2	MCF-7	breast:
5	chr11:47200274..47201665-chr11:47280495..47281727,7	MCF-7	breast:
6	chr11:47279843..47284326-chr11:47288675..47293634,16	MCF-7	breast:
7	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
8	chr11:47205592..47209017-chr11:47278399..47281373,5	MCF-7	breast:
9	chr11:47268496..47273681-chr11:47277782..47283365,10	K562	blood:
10	chr11:47277979..47283267-chr11:47289057..47293509,9	K562	blood:
11	chr11:47267134..47271941-chr11:47277592..47282899,11	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MADD-2	chr11:47280431-47280810	NONHSAT021225

No data

Variant related genes	Relation type
NR1H3	TF binding region
ENSG00000025434	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000256746	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000149182	Chromatin interaction
ENSG00000134575	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10838694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11039157	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11530168	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12573962	0.93[AMR][1000 genomes]
rs12575157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12575296	0.83[AMR][1000 genomes]
rs12576461	0.83[AMR][1000 genomes]
rs12576690	0.83[AMR][1000 genomes]
rs12576751	0.86[AMR][1000 genomes]
rs12577319	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17726390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17790420	1.00[YRI][hapmap]
rs2290149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs3736101	0.83[AMR][1000 genomes]
rs3758668	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3758671	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3758674	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816724	0.86[AMR][1000 genomes]
rs41301449	0.93[AMR][1000 genomes]
rs41304347	0.86[AMR][1000 genomes]
rs41310332	0.86[AMR][1000 genomes]
rs45489595	0.90[AMR][1000 genomes]
rs55764401	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56168519	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56177220	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56825896	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56886689	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61896015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61896047	0.93[AMR][1000 genomes]
rs61896051	0.86[AMR][1000 genomes]
rs61896053	0.83[AMR][1000 genomes]
rs61896054	0.83[AMR][1000 genomes]
rs61897361	0.83[AMR][1000 genomes]
rs7943429	0.83[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12221497	DGKZ	cis	cerebellum	SCAN
rs12221497	PTPRJ	cis	cerebellum	SCAN
rs12221497	VPS37B	trans	parietal	SCAN
rs12221497	PACSIN3	cis	Esophagus Mucosa	GTEx
rs12221497	MDK	cis	parietal	SCAN
rs12221497	ATG13	cis	parietal	SCAN
rs12221497	ATG13	cis	cerebellum	SCAN
rs12221497	MADD	cis	parietal	SCAN
rs12221497	NR1H3	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47271000-47280800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47271400-47281000	Weak transcription	Thymus	Thymus
3	chr11:47271400-47281200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr11:47271400-47281200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr11:47271400-47281200	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr11:47271400-47281200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:47272400-47286400	Weak transcription	Dnd41	blood
8	chr11:47275800-47286800	Weak transcription	Primary T cells from cord blood	blood
9	chr11:47276800-47280800	Weak transcription	HSMMtube	muscle
10	chr11:47277000-47282000	Weak transcription	Spleen	Spleen
11	chr11:47278600-47281600	Enhancers	Fetal Heart	heart
12	chr11:47278600-47282000	Flanking Active TSS	Hela-S3	cervix
13	chr11:47278800-47281000	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr11:47278800-47281600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr11:47278800-47281600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:47278800-47282000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:47278800-47282200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:47278800-47282200	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr11:47279000-47281600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr11:47279000-47281600	Enhancers	NH-A	brain
21	chr11:47279200-47288800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:47279400-47280800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:47279400-47280800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr11:47279400-47281200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:47279400-47281600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr11:47279400-47286800	Weak transcription	NHEK	skin
27	chr11:47279400-47289400	Weak transcription	Fetal Brain Female	brain
28	chr11:47279600-47281400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr11:47279800-47280800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr11:47279800-47280800	Weak transcription	Gastric	stomach
31	chr11:47279800-47281000	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr11:47279800-47281000	Flanking Active TSS	Fetal Intestine Large	intestine
33	chr11:47279800-47281200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr11:47279800-47281200	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr11:47279800-47281600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr11:47279800-47287000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr11:47279800-47289800	Weak transcription	Esophagus	oesophagus
38	chr11:47280000-47280800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr11:47280000-47280800	Enhancers	Primary hematopoietic stem cells	blood
40	chr11:47280000-47281000	Active TSS	Fetal Brain Male	brain
41	chr11:47280000-47281000	Enhancers	NHDF-Ad	bronchial
42	chr11:47280000-47281200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr11:47280000-47281200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr11:47280000-47281200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr11:47280000-47281200	Enhancers	Brain Cingulate Gyrus	brain
46	chr11:47280000-47281600	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr11:47280000-47281600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:47280000-47281600	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr11:47280000-47281600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:47280000-47281600	Enhancers	Brain Anterior Caudate	brain

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