Variant report

Variant	rs12664948
Chromosome Location	chr6:11431114-11431115
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11227633..11230379-chr6:11430461..11433425,2	MCF-7	breast:
2	chr6:11424461..11426917-chr6:11430880..11433034,2	K562	blood:
3	chr6:11415153..11417889-chr6:11429693..11432070,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233656	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs4076156	0.80[EUR][1000 genomes]
rs4301302	0.80[EUR][1000 genomes]
rs4318876	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4713507	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55918622	0.89[EUR][1000 genomes]
rs56155385	0.89[EUR][1000 genomes]
rs56317766	0.90[EUR][1000 genomes]
rs58289089	0.80[AMR][1000 genomes]
rs59286890	0.80[AMR][1000 genomes]
rs59349836	0.89[EUR][1000 genomes]
rs61650802	0.91[EUR][1000 genomes]
rs6909496	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72832944	0.91[EUR][1000 genomes]
rs72832950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12664948	C6orf218	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11423200-11431800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:11423400-11434200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:11423600-11432200	Enhancers	Muscle Satellite Cultured Cells	--
4	chr6:11423600-11435200	Enhancers	HepG2	liver
5	chr6:11423800-11435600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:11425000-11432200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:11425600-11436200	Enhancers	Adipose Nuclei	Adipose
8	chr6:11426400-11431800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:11427000-11432800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:11427400-11433400	Enhancers	NH-A	brain
11	chr6:11427800-11432000	Weak transcription	Aorta	Aorta
12	chr6:11428000-11434800	Weak transcription	Psoas Muscle	Psoas
13	chr6:11428000-11438000	Weak transcription	Esophagus	oesophagus
14	chr6:11428200-11432400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:11428200-11434400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:11428600-11433400	Weak transcription	Fetal Intestine Small	intestine
17	chr6:11428600-11434600	Weak transcription	Pancreas	Pancrea
18	chr6:11428800-11431600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:11428800-11431800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:11428800-11432800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:11429400-11431200	Enhancers	A549	lung
22	chr6:11429400-11432400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:11429400-11432400	Weak transcription	Left Ventricle	heart
24	chr6:11429400-11433000	Weak transcription	Brain Anterior Caudate	brain
25	chr6:11429400-11433400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:11429400-11434600	Weak transcription	Fetal Lung	lung
27	chr6:11429400-11434800	Weak transcription	Right Atrium	heart
28	chr6:11429400-11434800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:11429600-11432200	Weak transcription	HMEC	breast
30	chr6:11429600-11432800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:11429800-11432800	Weak transcription	HUVEC	blood vessel
32	chr6:11430000-11431200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:11430000-11431600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:11430000-11431800	Weak transcription	Hela-S3	cervix
35	chr6:11430000-11433000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr6:11430000-11435200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr6:11430000-11435800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:11430200-11432400	Weak transcription	Stomach Mucosa	stomach
39	chr6:11430200-11433600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:11430200-11434400	Weak transcription	Small Intestine	intestine
41	chr6:11430400-11432000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:11430400-11432000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:11430400-11433400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:11430600-11431200	Enhancers	GM12878-XiMat	blood
45	chr6:11430600-11431800	Weak transcription	HSMMtube	muscle
46	chr6:11430600-11431800	Weak transcription	NHDF-Ad	bronchial
47	chr6:11430600-11432000	Weak transcription	Placenta	Placenta
48	chr6:11430600-11432000	Weak transcription	NHLF	lung
49	chr6:11430600-11433000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:11430600-11433600	Weak transcription	Fetal Kidney	kidney

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