Variant report

Variant	rs10753798
Chromosome Location	chr1:169844515-169844516
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169844264..169846612-chr1:169869148..169870658,2	MCF-7	breast:
2	chr1:169841646..169845084-chr1:169857694..169862794,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10489177	0.81[CHB][hapmap]
rs10800477	0.81[CHB][hapmap]
rs10800478	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12128754	0.81[CHB][hapmap]
rs12760433	0.81[CHB][hapmap]
rs6704382	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7529874	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs882595	0.81[CHB][hapmap]
rs9803717	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9803860	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10753798	SCYL3	Cis_1M	lymphoblastoid	RTeQTL
rs10753798	C1orf156	cis	parietal	SCAN
rs10753798	C1orf156	cis	cerebellum	SCAN
rs10753798	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
4	chr1:169814400-169848600	Strong transcription	Duodenum Mucosa	Duodenum
5	chr1:169814800-169848000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:169815000-169845200	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr1:169815200-169848200	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:169815400-169848400	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:169817800-169848600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr1:169818200-169847800	Strong transcription	Adipose Nuclei	Adipose
11	chr1:169819000-169848200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:169819400-169847000	Strong transcription	Liver	Liver
13	chr1:169820400-169844800	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:169820400-169847200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:169820600-169847800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr1:169820600-169847800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:169820600-169848400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:169820600-169848600	Strong transcription	Fetal Lung	lung
19	chr1:169821600-169845200	Strong transcription	Stomach Smooth Muscle	stomach
20	chr1:169822000-169846000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:169822600-169845200	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:169825600-169845800	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:169826800-169848600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:169831800-169848400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:169833200-169845600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:169833400-169847000	Strong transcription	Left Ventricle	heart
27	chr1:169833800-169860200	Weak transcription	HMEC	breast
28	chr1:169834400-169846200	Strong transcription	HSMM	muscle
29	chr1:169834600-169845400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
30	chr1:169834800-169845200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:169837400-169848000	Strong transcription	Brain Anterior Caudate	brain
32	chr1:169837800-169845200	Strong transcription	HepG2	liver
33	chr1:169838000-169845000	Strong transcription	Right Ventricle	heart
34	chr1:169838800-169845000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr1:169840000-169846000	Strong transcription	Small Intestine	intestine
36	chr1:169840200-169845200	Strong transcription	Brain Hippocampus Middle	brain
37	chr1:169840400-169846600	Strong transcription	Fetal Stomach	stomach
38	chr1:169840600-169844800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:169841000-169845400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:169841000-169847200	Strong transcription	Brain Substantia Nigra	brain
41	chr1:169841000-169847400	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr1:169841400-169844800	Strong transcription	Hela-S3	cervix
43	chr1:169841400-169845200	Strong transcription	Fetal Kidney	kidney
44	chr1:169841600-169847000	Strong transcription	Ovary	ovary
45	chr1:169841600-169847200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:169841800-169844800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:169841800-169845200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:169841800-169845200	Strong transcription	Brain Germinal Matrix	brain
49	chr1:169841800-169845200	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:169841800-169845600	Strong transcription	Primary hematopoietic stem cells	blood

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