Variant report

Variant	rs2689680
Chromosome Location	chr1:77748786-77748787
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	chr1:77684670..77686781-chr1:77746398..77749229,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142892	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1010196	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10493603	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10747353	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10782646	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11162311	0.90[ASN][1000 genomes]
rs1167196	0.89[ASN][1000 genomes]
rs1167197	0.89[ASN][1000 genomes]
rs1167214	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12030598	0.94[JPT][hapmap]
rs12077615	0.90[ASN][1000 genomes]
rs12567557	0.88[JPT][hapmap]
rs12751884	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1377738	0.81[ASN][1000 genomes]
rs1453975	0.83[ASN][1000 genomes]
rs1453982	0.89[ASN][1000 genomes]
rs1619903	0.85[EUR][1000 genomes]
rs5018314	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7512141	0.90[ASN][1000 genomes]
rs7516300	0.91[ASN][1000 genomes]
rs7517051	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7517698	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7547493	0.94[JPT][hapmap]
rs7549462	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[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	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2689680	TYW3	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77746600-77749000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:77746800-77749200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:77746800-77749400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr1:77746800-77749600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:77747000-77749000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
6	chr1:77747000-77749400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:77747000-77749600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr1:77747000-77750400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr1:77747000-77750600	Active TSS	Brain Substantia Nigra	brain
10	chr1:77747200-77748800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:77747200-77748800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:77747200-77748800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
13	chr1:77747200-77748800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
14	chr1:77747200-77748800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
15	chr1:77747200-77748800	Active TSS	A549	lung
16	chr1:77747200-77749000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:77747200-77749000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr1:77747200-77749000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:77747200-77749000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
20	chr1:77747200-77749000	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr1:77747200-77749000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
22	chr1:77747200-77749000	Active TSS	NHLF	lung
23	chr1:77747200-77749200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr1:77747200-77749200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:77747200-77749200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:77747200-77749200	Active TSS	HSMM	muscle
27	chr1:77747200-77749200	Active TSS	HSMMtube	muscle
28	chr1:77747200-77751000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:77747400-77748800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:77747400-77748800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:77747400-77748800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
32	chr1:77747400-77749000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr1:77747400-77749000	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr1:77747400-77749000	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:77747400-77749000	Active TSS	Aorta	Aorta
36	chr1:77747400-77749000	Active TSS	Osteobl	bone
37	chr1:77747400-77749200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:77747400-77749200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:77747400-77749200	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
40	chr1:77747400-77749200	Active TSS	NHDF-Ad	bronchial
41	chr1:77747400-77749400	Active TSS	H9 Cell Line	embryonic stem cell
42	chr1:77747400-77750000	Active TSS	Muscle Satellite Cultured Cells	--
43	chr1:77747400-77750200	Active TSS	Brain Hippocampus Middle	brain
44	chr1:77747400-77750400	Active TSS	Brain Angular Gyrus	brain
45	chr1:77747400-77750600	Active TSS	Brain Cingulate Gyrus	brain
46	chr1:77747600-77749000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr1:77747600-77749000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:77747600-77749000	Flanking Bivalent TSS/Enh	Right Ventricle	heart
49	chr1:77747600-77749200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:77747600-77749200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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