Variant report

Variant	rs416768
Chromosome Location	chr1:220863371-220863372
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220862132..220866220-chr1:220920879..220923309,4	MCF-7	breast:
2	chr1:220863249..220864128-chr1:220950068..220950638,2	K562	blood:

Variant related genes	Relation type
ENSG00000117791	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12030411	0.97[ASN][1000 genomes]
rs12034388	0.85[CEU][hapmap]
rs17008307	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.82[MKK][hapmap];0.92[ASN][1000 genomes]
rs2960571	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs337180	0.83[ASN][1000 genomes]
rs364360	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs384264	0.96[ASN][1000 genomes]
rs405682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs409286	0.96[ASN][1000 genomes]
rs413426	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs425437	0.92[ASW][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs437078	0.92[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs700036	0.88[ASN][1000 genomes]
rs774128	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs774130	0.97[ASN][1000 genomes]
rs9431295	0.93[ASW][hapmap];0.85[YRI][hapmap];0.86[AFR][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	nsv468194	chr1:220845610-220885612	Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv549227	chr1:220845610-220885612	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv2754270	chr1:220850116-220929155	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs416768	MOSC1	cis	multi-tissue	Pritchard
rs416768	MOSC2	cis	multi-tissue	Pritchard
rs416768	FLJ14146	cis	multi-tissue	Pritchard
rs416768	MOSC1	cis	Lymphoblastoid	GTEx
rs416768	C1orf115	cis	multi-tissue	Pritchard
rs416768	C1orf115	cis	Lymphoblastoid	GTEx
rs416768	MOSC2	cis	Lymphoblastoid	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220863000-220863400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
2	chr1:220863000-220863400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:220863000-220863400	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
4	chr1:220863000-220863400	Flanking Active TSS	Fetal Brain Female	brain
5	chr1:220863000-220863400	Bivalent Enhancer	Fetal Thymus	thymus
6	chr1:220863000-220863400	Enhancers	Small Intestine	intestine
7	chr1:220863000-220863400	Enhancers	Spleen	Spleen
8	chr1:220863000-220863600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:220863000-220863600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr1:220863000-220863600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr1:220863000-220863600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr1:220863000-220863600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr1:220863000-220863600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:220863000-220863600	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr1:220863000-220863600	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr1:220863000-220863600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr1:220863000-220863600	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
18	chr1:220863000-220863600	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr1:220863000-220863600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr1:220863000-220863600	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial
21	chr1:220863000-220864000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:220863000-220864000	Active TSS	Brain Anterior Caudate	brain
23	chr1:220863000-220864600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
24	chr1:220863000-220864600	Active TSS	H9 Cell Line	embryonic stem cell
25	chr1:220863000-220864600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr1:220863000-220864800	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr1:220863000-220865000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:220863000-220865200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr1:220863000-220865200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr1:220863000-220865200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
31	chr1:220863000-220865200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr1:220863000-220866000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:220863200-220863400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:220863200-220863400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:220863200-220863400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:220863200-220863400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:220863200-220863400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr1:220863200-220863400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
39	chr1:220863200-220863400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
40	chr1:220863200-220863400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
41	chr1:220863200-220863400	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:220863200-220863400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
43	chr1:220863200-220863400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
44	chr1:220863200-220863400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr1:220863200-220863400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:220863200-220863400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:220863200-220863400	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr1:220863200-220863400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
49	chr1:220863200-220863400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
50	chr1:220863200-220863400	Flanking Active TSS	Fetal Heart	heart

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