Variant report

Variant	rs6696683
Chromosome Location	chr1:225817131-225817132
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225812888..225814596-chr1:225815974..225818841,2	MCF-7	breast:
2	chr1:225817081..225819412-chr1:226067962..226070291,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196187	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11801322	0.97[AFR][1000 genomes]
rs11808089	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617210	0.91[AFR][1000 genomes]
rs55865602	0.84[AFR][1000 genomes]
rs55893672	0.85[AFR][1000 genomes]
rs57616580	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58221350	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58384340	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59481688	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60271197	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60588592	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666276	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687755	0.90[AFR][1000 genomes]
rs6687947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698989	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6702446	1.00[ASN][1000 genomes]
rs73124025	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73125705	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73125706	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73125707	0.84[AFR][1000 genomes]
rs7515673	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531033	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555097	0.93[AMR][1000 genomes];1.00[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	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
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:225781000-225825400	Weak transcription	Fetal Stomach	stomach
3	chr1:225806200-225817600	Weak transcription	Fetal Brain Female	brain
4	chr1:225807200-225820400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:225808200-225818400	Weak transcription	Fetal Brain Male	brain
6	chr1:225809800-225837800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:225810000-225825400	Weak transcription	NHEK	skin
8	chr1:225812800-225824400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:225812800-225825000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:225813400-225824800	Weak transcription	Lung	lung
11	chr1:225813600-225837600	Weak transcription	HUVEC	blood vessel
12	chr1:225813800-225817200	Enhancers	Psoas Muscle	Psoas
13	chr1:225813800-225838600	Weak transcription	HMEC	breast
14	chr1:225814200-225818800	Weak transcription	Gastric	stomach
15	chr1:225814200-225819600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:225814400-225820400	Weak transcription	HSMM	muscle
17	chr1:225814400-225825200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:225814400-225825400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:225814600-225818200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:225814600-225818800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:225814600-225835800	Weak transcription	HSMMtube	muscle
22	chr1:225815400-225823200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:225815400-225823800	Weak transcription	NH-A	brain
24	chr1:225815600-225817600	Weak transcription	NHDF-Ad	bronchial
25	chr1:225815600-225819800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:225815600-225822800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:225815600-225825400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:225815600-225830000	Weak transcription	Pancreas	Pancrea
29	chr1:225815800-225817400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:225815800-225818000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:225815800-225818600	Weak transcription	Fetal Lung	lung
32	chr1:225815800-225818800	Weak transcription	Left Ventricle	heart
33	chr1:225815800-225819800	Weak transcription	Brain Anterior Caudate	brain
34	chr1:225815800-225820000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:225815800-225823200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:225815800-225823400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:225815800-225823400	Weak transcription	Stomach Mucosa	stomach
38	chr1:225815800-225825400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:225815800-225839000	Weak transcription	Fetal Intestine Large	intestine
40	chr1:225816000-225818000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:225816000-225818600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:225816000-225818800	Weak transcription	Fetal Intestine Small	intestine
43	chr1:225816000-225819000	Weak transcription	Ovary	ovary
44	chr1:225816000-225825600	Weak transcription	Fetal Muscle Leg	muscle
45	chr1:225816000-225825800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:225816000-225825800	Weak transcription	HepG2	liver
47	chr1:225816000-225830000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:225816000-225832400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:225816000-225834200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:225816000-225838400	Weak transcription	H9 Cell Line	embryonic stem cell

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