Variant report

Variant	rs11834543
Chromosome Location	chr12:49618043-49618044
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49519485..49526890-chr12:49616239..49624332,15	K562	blood:
2	chr12:49617947..49619571-chr12:49625520..49628045,3	K562	blood:
3	chr12:49608287..49610880-chr12:49615814..49620950,5	K562	blood:
4	chr12:49608287..49611416-chr12:49615384..49618103,4	K562	blood:
5	chr12:49617947..49619523-chr12:49625520..49627493,2	K562	blood:
6	chr12:49513866..49528454-chr12:49616957..49635747,92	K562	blood:
7	chr12:49617540..49619785-chr12:49657644..49659586,2	K562	blood:

Variant related genes	Relation type
ENSG00000167553	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000200309	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10783310	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10875937	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168948	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11834620	0.88[ASN][1000 genomes]
rs17123623	0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs2335453	0.83[ASN][1000 genomes]
rs7133057	0.85[ASN][1000 genomes]
rs7971455	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv518041	chr12:49618043-49645240	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11834543	MLL2	cis	cerebellum	SCAN
rs11834543	WNT1	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49610200-49625800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:49612200-49620200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:49614200-49618400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr12:49615200-49618600	Enhancers	Fetal Muscle Leg	muscle
5	chr12:49615200-49625600	Weak transcription	Placenta	Placenta
6	chr12:49616000-49618400	Enhancers	Fetal Muscle Trunk	muscle
7	chr12:49616400-49618400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr12:49616400-49619800	Enhancers	Brain Hippocampus Middle	brain
9	chr12:49616600-49619000	Weak transcription	K562	blood
10	chr12:49616800-49618800	Weak transcription	HMEC	breast
11	chr12:49616800-49619400	Weak transcription	A549	lung
12	chr12:49616800-49621000	Weak transcription	Fetal Brain Female	brain
13	chr12:49616800-49624400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:49616800-49625800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr12:49616800-49626000	Weak transcription	Adipose Nuclei	Adipose
16	chr12:49617000-49618400	Enhancers	HSMMtube	muscle
17	chr12:49617000-49618600	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr12:49617000-49619400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr12:49617000-49619400	Weak transcription	NHEK	skin
20	chr12:49617000-49619600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:49617000-49619600	Weak transcription	Fetal Thymus	thymus
22	chr12:49617000-49624000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:49617200-49619400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:49617200-49619400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:49617200-49619400	Weak transcription	Osteobl	bone
26	chr12:49617200-49619600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:49617200-49620000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr12:49617400-49618200	Weak transcription	Spleen	Spleen
29	chr12:49617400-49619400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:49617400-49619600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:49617600-49619400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:49617600-49620800	Weak transcription	Fetal Brain Male	brain
33	chr12:49617600-49625600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:49617600-49625800	Weak transcription	NHDF-Ad	bronchial
35	chr12:49617600-49626000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:49617800-49619000	Weak transcription	NHLF	lung
37	chr12:49617800-49619400	Weak transcription	HSMM	muscle
38	chr12:49617800-49620800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:49617800-49621400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:49617800-49621400	Weak transcription	Brain Angular Gyrus	brain
41	chr12:49617800-49621400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr12:49617800-49621400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:49618000-49618400	Weak transcription	Primary B cells from cord blood	blood
44	chr12:49618000-49619400	Weak transcription	Brain Substantia Nigra	brain
45	chr12:49618000-49620600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:49618000-49621400	Weak transcription	Brain Anterior Caudate	brain

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