Variant report

Variant	rs2996683
Chromosome Location	chr1:209380966-209380967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209249394..209250232-chr1:209380730..209381661,2	MCF-7	breast:
2	chr1:209379971..209382311-chr1:209606603..209608628,2	MCF-7	breast:
3	chr1:209380711..209382110-chr1:209421741..209422984,5	MCF-7	breast:
4	chr1:208825434..208826290-chr1:209380727..209381616,2	MCF-7	breast:
5	chr1:209249788..209250661-chr1:209380684..209381520,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1933619	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2250701	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2266024	0.84[EUR][1000 genomes]
rs2489651	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2788152	0.81[CEU][hapmap]
rs2788158	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2788159	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2788161	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2788162	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2788168	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2788170	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2970555	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2970556	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2970560	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2996687	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2996688	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34523921	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34944110	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4396124	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6658956	1.00[CHB][hapmap]
rs6672407	1.00[CHB][hapmap]
rs66763810	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71636106	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832481	chr1:209371276-209540333	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209373200-209381200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:209377200-209381200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:209380200-209381200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
4	chr1:209380400-209381000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:209380400-209381200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:209380400-209381400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:209380400-209381400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:209380400-209381800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:209380600-209381000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
10	chr1:209380600-209381000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:209380600-209381000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr1:209380600-209381000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:209380600-209381000	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr1:209380600-209381000	Flanking Active TSS	Brain Cingulate Gyrus	brain
15	chr1:209380600-209381000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
16	chr1:209380600-209381000	Bivalent Enhancer	Fetal Stomach	stomach
17	chr1:209380600-209381000	Enhancers	Spleen	Spleen
18	chr1:209380600-209381200	Enhancers	H9 Cell Line	embryonic stem cell
19	chr1:209380600-209381200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
20	chr1:209380600-209381200	Enhancers	Primary hematopoietic stem cells	blood
21	chr1:209380600-209381200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:209380600-209381200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr1:209380600-209381200	Bivalent Enhancer	Fetal Intestine Small	intestine
24	chr1:209380600-209381200	Enhancers	Fetal Thymus	thymus
25	chr1:209380600-209381400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:209380600-209381400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:209380600-209381400	Active TSS	Brain Substantia Nigra	brain
28	chr1:209380600-209381400	Bivalent/Poised TSS	HepG2	liver
29	chr1:209380600-209381400	Active TSS	NHDF-Ad	bronchial
30	chr1:209380600-209381600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
31	chr1:209380600-209381600	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr1:209380600-209381800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr1:209380600-209381800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
34	chr1:209380800-209381000	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
35	chr1:209380800-209381000	Enhancers	H1 Cell Line	embryonic stem cell
36	chr1:209380800-209381000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
37	chr1:209380800-209381000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
38	chr1:209380800-209381000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr1:209380800-209381000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:209380800-209381000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:209380800-209381000	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr1:209380800-209381000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr1:209380800-209381000	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr1:209380800-209381000	Flanking Active TSS	Fetal Brain Male	brain
45	chr1:209380800-209381000	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
46	chr1:209380800-209381000	Flanking Active TSS	Fetal Lung	lung
47	chr1:209380800-209381000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
48	chr1:209380800-209381000	Flanking Bivalent TSS/Enh	Left Ventricle	heart
49	chr1:209380800-209381000	Flanking Active TSS	Ovary	ovary
50	chr1:209380800-209381000	Enhancers	Rectal Smooth Muscle	rectum

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