Variant report

Variant	rs12225782
Chromosome Location	chr11:85964685-85964686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85953211..85960614-chr11:85961214..85967523,10	K562	blood:
2	chr11:85953211..85956720-chr11:85962285..85965170,5	K562	blood:

Variant related genes	Relation type
ENSG00000074266	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10792840	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898450	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898455	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234582	0.92[CEU][hapmap];0.92[CHD][hapmap]
rs11234583	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11234585	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11234586	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11234587	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11234591	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11234595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1215001	0.87[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12226796	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12282663	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12574118	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12577739	0.90[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12800606	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1376947	1.00[ASW][hapmap];0.87[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1391221	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs19039	1.00[ASW][hapmap];0.83[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2173281	0.87[CHD][hapmap]
rs2847470	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs291215	0.92[CHB][hapmap]
rs291216	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs291220	0.93[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs291221	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs291225	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs291227	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291228	0.87[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291230	0.83[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291231	0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs291232	0.86[EUR][1000 genomes]
rs291233	0.83[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291234	0.83[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs291235	0.87[EUR][1000 genomes]
rs291236	0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs291237	0.87[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs291238	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs291242	0.83[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs291247	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs291251	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34095340	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34972740	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3923738	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547120	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944562	0.98[EUR][1000 genomes]
rs7106569	0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv832223	chr11:85845315-86015957	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12225782	EED	cis	parietal	SCAN
rs12225782	EED	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85957200-85972400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:85957200-85972400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:85957200-85972400	Weak transcription	Esophagus	oesophagus
4	chr11:85957200-85995400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:85957400-85967600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr11:85957400-85985600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:85957400-86008000	Weak transcription	Psoas Muscle	Psoas
8	chr11:85957800-85967800	Weak transcription	Thymus	Thymus
9	chr11:85957800-85968000	Weak transcription	HSMMtube	muscle
10	chr11:85957800-85968600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:85957800-85968600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr11:85957800-85997200	Weak transcription	Colonic Mucosa	Colon
13	chr11:85957800-85999800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr11:85958400-85966200	Weak transcription	NH-A	brain
15	chr11:85958400-85966400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr11:85958400-85972400	Weak transcription	Aorta	Aorta
17	chr11:85958400-85997200	Weak transcription	Brain Germinal Matrix	brain
18	chr11:85958800-85967000	Weak transcription	HSMM	muscle
19	chr11:85959200-85967000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr11:85959200-85967000	Weak transcription	Fetal Muscle Leg	muscle
21	chr11:85959200-85967800	Weak transcription	Fetal Intestine Large	intestine
22	chr11:85959200-85974000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr11:85959200-85988000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr11:85959200-85988600	Weak transcription	Brain Angular Gyrus	brain
25	chr11:85959200-85997600	Weak transcription	Colon Smooth Muscle	Colon
26	chr11:85959400-85967400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr11:85959400-85995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr11:85960000-85968000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr11:85960000-85970800	Weak transcription	Fetal Brain Female	brain
30	chr11:85960000-85972400	Weak transcription	Pancreas	Pancrea
31	chr11:85960200-85966800	Weak transcription	Liver	Liver
32	chr11:85960200-85967000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:85960200-85967200	Weak transcription	HepG2	liver
34	chr11:85960200-85967400	Weak transcription	Left Ventricle	heart
35	chr11:85960200-85967400	Weak transcription	HMEC	breast
36	chr11:85960200-85968000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr11:85960200-85968000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:85960200-85972800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr11:85960200-85985600	Weak transcription	Gastric	stomach
40	chr11:85960600-85966400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:85960600-85967400	Weak transcription	HUVEC	blood vessel
42	chr11:85960600-85972200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:85960800-85967000	Weak transcription	Adipose Nuclei	Adipose
44	chr11:85960800-85972400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:85960800-85988000	Weak transcription	Fetal Heart	heart
46	chr11:85961000-85967400	Weak transcription	Fetal Kidney	kidney
47	chr11:85961000-85968000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:85961000-85968000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:85961000-85972200	Weak transcription	Ovary	ovary
50	chr11:85961000-85972400	Weak transcription	Right Ventricle	heart

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