Variant report

Variant	rs1053221
Chromosome Location	chr1:241755567-241755568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:241754919..241756738-chr1:241772930..241774735,2	MCF-7	breast:
2	chr1:241752654..241756956-chr1:241801862..241804156,4	MCF-7	breast:
3	chr1:241692640..241698484-chr1:241752819..241757508,7	MCF-7	breast:
4	chr1:241702260..241709454-chr1:241751164..241757390,11	MCF-7	breast:
5	chr1:241692675..241699772-chr1:241751334..241757827,9	MCF-7	breast:
6	chr1:241703983..241707059-chr1:241753583..241756935,3	MCF-7	breast:
7	chr1:241745082..241748095-chr1:241752482..241756598,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117009	Chromatin interaction
ENSG00000054277	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10926521	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10926523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12030098	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12128430	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12139441	0.82[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12144172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3193688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3765807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7349139	0.92[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	nsv427963	chr1:241718799-241832833	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1053221	SLC16A6	trans	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241740200-241759600	Strong transcription	Primary B cells from peripheral blood	blood
2	chr1:241740400-241768800	Weak transcription	Spleen	Spleen
3	chr1:241742000-241757400	Weak transcription	Primary T cells from cord blood	blood
4	chr1:241743000-241757400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:241743200-241768600	Weak transcription	Esophagus	oesophagus
6	chr1:241746600-241779200	Weak transcription	Lung	lung
7	chr1:241746800-241761400	Weak transcription	GM12878-XiMat	blood
8	chr1:241746800-241779600	Weak transcription	Aorta	Aorta
9	chr1:241747000-241757200	Weak transcription	HUVEC	blood vessel
10	chr1:241749200-241760000	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:241749400-241757200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:241749400-241760200	Strong transcription	Liver	Liver
13	chr1:241750000-241759600	Strong transcription	Primary B cells from cord blood	blood
14	chr1:241750400-241757000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:241750600-241771600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:241750600-241786000	Weak transcription	Fetal Brain Female	brain
17	chr1:241750800-241759200	Weak transcription	Fetal Brain Male	brain
18	chr1:241750800-241768800	Weak transcription	Fetal Kidney	kidney
19	chr1:241750800-241771800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:241750800-241773400	Weak transcription	Brain Angular Gyrus	brain
21	chr1:241750800-241774600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:241750800-241786200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:241752600-241773400	Weak transcription	Gastric	stomach
24	chr1:241753200-241757800	Enhancers	HMEC	breast
25	chr1:241753400-241761000	Weak transcription	HepG2	liver
26	chr1:241753400-241791200	Weak transcription	Thymus	Thymus
27	chr1:241753600-241757000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:241753600-241757000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:241753600-241757200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:241753600-241757400	Enhancers	NHEK	skin
31	chr1:241753800-241755800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr1:241753800-241757200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:241753800-241759600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:241754000-241756400	Genic enhancers	Primary monocytes fromperipheralblood	blood
35	chr1:241754000-241757200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:241754000-241757400	Enhancers	Hela-S3	cervix
37	chr1:241754000-241757800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:241754200-241759400	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:241754200-241759600	Weak transcription	K562	blood
40	chr1:241754200-241773600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:241754400-241757200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:241754400-241760000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:241754400-241782600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:241754600-241755800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:241754800-241757200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr1:241754800-241760000	Weak transcription	Fetal Intestine Small	intestine
47	chr1:241755000-241756000	Enhancers	NH-A	brain
48	chr1:241755000-241756400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:241755000-241756600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:241755000-241757000	Enhancers	NHDF-Ad	bronchial

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