Variant report

Variant	rs405682
Chromosome Location	chr1:220864724-220864725
allele	C/T
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:

Variant related genes	Relation type
ENSG00000117791	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs12030411	0.98[ASN][1000 genomes]
rs12034388	0.85[CEU][hapmap]
rs17008307	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2960571	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337180	0.83[ASN][1000 genomes]
rs364360	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384264	0.96[ASN][1000 genomes]
rs409286	0.96[ASN][1000 genomes]
rs413426	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs416768	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]
rs425437	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs437078	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs700036	0.89[ASN][1000 genomes]
rs774128	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs774130	0.98[ASN][1000 genomes]
rs9431295	0.84[YRI][hapmap];0.80[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs405682	C1orf115	cis	multi-tissue	Pritchard
rs405682	MOSC1	cis	Lymphoblastoid	GTEx
rs405682	MOSC2	cis	Lymphoblastoid	GTEx
rs405682	MOSC2	cis	multi-tissue	Pritchard
rs405682	MOSC1	cis	multi-tissue	Pritchard
rs405682	C1orf115	cis	Lymphoblastoid	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220863000-220864800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:220863000-220865000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:220863000-220865200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:220863000-220865200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr1:220863000-220865200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr1:220863000-220865200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:220863000-220866000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:220863200-220864800	Active TSS	Right Atrium	heart
9	chr1:220863400-220865000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:220863400-220865000	Active TSS	Fetal Intestine Small	intestine
11	chr1:220863400-220865000	Active TSS	Lung	lung
12	chr1:220863400-220865200	Active TSS	Fetal Brain Female	brain
13	chr1:220863400-220865200	Active TSS	Fetal Kidney	kidney
14	chr1:220863400-220865200	Active TSS	Ovary	ovary
15	chr1:220863400-220865200	Active TSS	Rectal Smooth Muscle	rectum
16	chr1:220863400-220865200	Active TSS	Spleen	Spleen
17	chr1:220863400-220865400	Active TSS	Brain Angular Gyrus	brain
18	chr1:220863400-220866800	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr1:220863600-220864800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:220863600-220864800	Active TSS	Left Ventricle	heart
21	chr1:220863600-220864800	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr1:220863600-220864800	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr1:220863600-220864800	Active TSS	Stomach Mucosa	stomach
24	chr1:220863600-220864800	Bivalent/Poised TSS	HepG2	liver
25	chr1:220863600-220865400	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr1:220863600-220865400	Active TSS	Right Ventricle	heart
27	chr1:220863600-220866000	Active TSS	Brain Cingulate Gyrus	brain
28	chr1:220863600-220866200	Active TSS	Duodenum Mucosa	Duodenum
29	chr1:220863600-220866200	Active TSS	Fetal Intestine Large	intestine
30	chr1:220863600-220866600	Active TSS	Placenta	Placenta
31	chr1:220863800-220865000	Active TSS	Psoas Muscle	Psoas
32	chr1:220863800-220865600	Enhancers	Fetal Brain Male	brain
33	chr1:220864200-220865000	Flanking Active TSS	HUVEC	blood vessel
34	chr1:220864200-220865400	Active TSS	Colonic Mucosa	Colon
35	chr1:220864200-220870000	Weak transcription	Aorta	Aorta
36	chr1:220864400-220864800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
37	chr1:220864400-220864800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr1:220864400-220864800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
39	chr1:220864400-220864800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr1:220864400-220864800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:220864400-220864800	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr1:220864400-220864800	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
43	chr1:220864400-220865000	Bivalent/Poised TSS	Primary B cells from cord blood	blood
44	chr1:220864400-220865000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr1:220864400-220865000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:220864400-220865000	Active TSS	Brain Hippocampus Middle	brain
47	chr1:220864400-220865000	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr1:220864400-220865200	Enhancers	Primary B cells from peripheral blood	blood
49	chr1:220864400-220865200	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
50	chr1:220864400-220865400	Active TSS	Brain Anterior Caudate	brain

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