Variant report

Variant	rs2769689
Chromosome Location	chr1:225797957-225797958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225777772..225779760-chr1:225795997..225798741,2	MCF-7	breast:
2	chr1:225792909..225795707-chr1:225797297..225800991,3	K562	blood:
3	chr1:225792350..225796305-chr1:225796696..225799620,4	MCF-7	breast:
4	chr1:225724969..225726561-chr1:225797392..225799589,2	MCF-7	breast:

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1075364	0.80[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2840959	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2840966	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2769689	TAF1A	cis	parietal	SCAN
rs2769689	C1orf55	cis	parietal	SCAN
rs2769689	FAM177B	cis	cerebellum	SCAN
rs2769689	LBR	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225748800-225799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:225768800-225805600	Weak transcription	Aorta	Aorta
4	chr1:225780800-225815400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:225781000-225825400	Weak transcription	Fetal Stomach	stomach
6	chr1:225782400-225806200	Weak transcription	Right Ventricle	heart
7	chr1:225784200-225807800	Weak transcription	Fetal Brain Male	brain
8	chr1:225785200-225800000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:225791200-225798800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:225791600-225799600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:225791600-225802000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:225792000-225799600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:225792000-225805000	Weak transcription	NHDF-Ad	bronchial
14	chr1:225792200-225800000	Weak transcription	Hela-S3	cervix
15	chr1:225792800-225799600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:225793000-225799200	Weak transcription	NHEK	skin
17	chr1:225793200-225799600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:225793600-225798400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:225793600-225799400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:225793600-225813200	Weak transcription	Left Ventricle	heart
21	chr1:225793600-225813800	Weak transcription	NH-A	brain
22	chr1:225794400-225800000	Weak transcription	Spleen	Spleen
23	chr1:225794600-225800000	Weak transcription	Pancreas	Pancrea
24	chr1:225794600-225813200	Weak transcription	Lung	lung
25	chr1:225794800-225798600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr1:225795000-225806000	Weak transcription	Small Intestine	intestine
27	chr1:225795600-225798600	Weak transcription	HSMM	muscle
28	chr1:225795600-225799600	Weak transcription	HepG2	liver
29	chr1:225795600-225800000	Weak transcription	Gastric	stomach
30	chr1:225795600-225802200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:225795600-225805000	Weak transcription	HSMMtube	muscle
32	chr1:225795600-225805400	Weak transcription	NHLF	lung
33	chr1:225795600-225813200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:225795600-225813200	Weak transcription	Psoas Muscle	Psoas
35	chr1:225795600-225813800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:225795800-225798000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:225795800-225802000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:225795800-225802000	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:225796400-225800000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:225796400-225802000	Weak transcription	Fetal Muscle Leg	muscle
41	chr1:225796400-225810200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:225796400-225812600	Weak transcription	Right Atrium	heart
43	chr1:225796600-225799400	Weak transcription	Ovary	ovary
44	chr1:225796600-225812200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr1:225797000-225802200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:225797200-225798000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:225797200-225798000	Weak transcription	Osteobl	bone
48	chr1:225797200-225798400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:225797200-225798800	Enhancers	A549	lung
50	chr1:225797200-225799400	Weak transcription	Fetal Lung	lung

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