Variant report

Variant	rs11054874
Chromosome Location	chr12:12543233-12543234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10505766	1.00[JPT][hapmap]
rs10743984	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10743986	0.82[CEU][hapmap];0.89[ASN][1000 genomes]
rs10743987	1.00[CHB][hapmap]
rs10772558	0.83[EUR][1000 genomes]
rs10772564	0.89[ASN][1000 genomes]
rs10772565	0.89[ASN][1000 genomes]
rs10845531	0.83[AMR][1000 genomes]
rs10845534	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap]
rs10845538	0.89[ASN][1000 genomes]
rs10845549	1.00[JPT][hapmap]
rs10845550	1.00[CHB][hapmap]
rs11054879	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11054898	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11054900	0.89[ASN][1000 genomes]
rs11054902	0.89[ASN][1000 genomes]
rs11054904	0.89[ASN][1000 genomes]
rs11054917	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11054918	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs12301872	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes]
rs2111270	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs918115	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS 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
2	nsv898808	chr12:12463407-12549503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1045637	chr12:12506839-12546747	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	esv2760275	chr12:12530073-12546759	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv437141	chr12:12530718-12544266	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv557593	chr12:12532984-12543233	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv818895	chr12:12532984-12544266	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv517152	chr12:12532984-12547645	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1041842	chr12:12536207-12546747	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv557597	chr12:12537608-12543233	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv557599	chr12:12537838-12543233	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv557603	chr12:12538410-12543233	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv557606	chr12:12540376-12543233	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11054874	LOH12CR1	cis	parietal	SCAN
rs11054874	ETV6	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12511600-12550600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:12512000-12545000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:12519200-12549800	Weak transcription	Aorta	Aorta
4	chr12:12521800-12556200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:12525400-12550200	Weak transcription	Fetal Stomach	stomach
6	chr12:12526400-12558800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:12532800-12556400	Weak transcription	Spleen	Spleen
8	chr12:12533000-12545800	Weak transcription	Pancreas	Pancrea
9	chr12:12533400-12555800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr12:12533600-12555400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr12:12535400-12561400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:12537200-12576000	Weak transcription	Primary B cells from cord blood	blood
13	chr12:12538200-12551000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:12538400-12545800	Weak transcription	Left Ventricle	heart
15	chr12:12538400-12548600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:12538400-12549200	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:12538400-12550200	Weak transcription	Primary T cells from cord blood	blood
18	chr12:12538400-12551600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:12538400-12552800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:12538400-12555400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:12538400-12556200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:12538600-12561800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:12538800-12551400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr12:12539400-12546800	Weak transcription	Stomach Mucosa	stomach
25	chr12:12539600-12545200	Weak transcription	Fetal Intestine Small	intestine
26	chr12:12539800-12545800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr12:12540200-12545000	Weak transcription	HepG2	liver
28	chr12:12540200-12545200	Weak transcription	Fetal Intestine Large	intestine
29	chr12:12540200-12560600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:12540600-12549400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:12540600-12556200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:12540800-12543600	Weak transcription	Thymus	Thymus
33	chr12:12540800-12543800	Weak transcription	Fetal Thymus	thymus
34	chr12:12540800-12550800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:12540800-12551000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr12:12540800-12553800	Weak transcription	GM12878-XiMat	blood
37	chr12:12540800-12555400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr12:12541000-12543600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:12541000-12543800	Weak transcription	K562	blood
40	chr12:12541000-12545000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:12541000-12545000	Weak transcription	Fetal Lung	lung
42	chr12:12541000-12545200	Weak transcription	Fetal Heart	heart
43	chr12:12541000-12550000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:12541000-12550200	Weak transcription	Hela-S3	cervix
45	chr12:12541000-12550600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:12541000-12551000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:12541000-12551000	Weak transcription	Small Intestine	intestine
48	chr12:12541200-12545200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr12:12541200-12547000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr12:12541200-12549200	Weak transcription	NHLF	lung

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