Variant report

Variant	rs672606
Chromosome Location	chr1:10526144-10526145
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	chr1:10523590..10526490-chr1:10532101..10535052,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142655	Chromatin interaction
ENSG00000160049	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10746494	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10864458	0.83[AFR][1000 genomes]
rs11121579	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1203122	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12565133	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1307485	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1307487	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1750349	0.81[ASN][1000 genomes]
rs1760664	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2186949	0.83[EUR][1000 genomes]
rs2483684	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2781233	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36013615	0.81[EUR][1000 genomes]
rs475549	0.84[EUR][1000 genomes]
rs481571	0.86[EUR][1000 genomes]
rs491880	0.84[EUR][1000 genomes]
rs505141	0.86[EUR][1000 genomes]
rs519472	0.86[EUR][1000 genomes]
rs520964	0.83[EUR][1000 genomes]
rs522029	0.84[EUR][1000 genomes]
rs522280	0.86[EUR][1000 genomes]
rs524150	0.86[EUR][1000 genomes]
rs528713	0.86[EUR][1000 genomes]
rs583515	0.83[EUR][1000 genomes]
rs586223	0.86[EUR][1000 genomes]
rs628462	0.80[ASN][1000 genomes]
rs632690	0.83[EUR][1000 genomes]
rs634358	0.86[EUR][1000 genomes]
rs643400	0.80[EUR][1000 genomes]
rs649101	0.86[EUR][1000 genomes]
rs649639	0.86[EUR][1000 genomes]
rs655271	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs663864	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs666583	0.84[EUR][1000 genomes]
rs670666	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs673254	0.91[EUR][1000 genomes]
rs678850	0.86[EUR][1000 genomes]
rs681448	0.83[EUR][1000 genomes]
rs684016	0.86[EUR][1000 genomes]
rs685746	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10499200-10531400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:10510600-10531600	Weak transcription	Right Atrium	heart
3	chr1:10511600-10531600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:10512400-10531200	Weak transcription	Fetal Brain Male	brain
5	chr1:10516000-10530200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:10516000-10530200	Strong transcription	Fetal Stomach	stomach
7	chr1:10516800-10528000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:10516800-10530200	Strong transcription	Fetal Muscle Trunk	muscle
9	chr1:10516800-10530400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:10517000-10529800	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr1:10517200-10529400	Strong transcription	Brain Germinal Matrix	brain
12	chr1:10517400-10531600	Weak transcription	Fetal Heart	heart
13	chr1:10517600-10529600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:10517800-10527800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:10517800-10530400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:10518000-10529200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:10518000-10529600	Strong transcription	H9 Cell Line	embryonic stem cell
18	chr1:10518000-10529600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:10518000-10530400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:10518200-10530200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:10519000-10529200	Strong transcription	Fetal Thymus	thymus
22	chr1:10519000-10529400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:10519000-10529800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:10519200-10529600	Strong transcription	Thymus	Thymus
25	chr1:10519600-10530600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:10519800-10531400	Weak transcription	Stomach Mucosa	stomach
27	chr1:10520000-10531200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:10520000-10531400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:10520200-10531200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:10520400-10529600	Strong transcription	Brain Hippocampus Middle	brain
31	chr1:10520400-10530000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:10520600-10526800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:10520600-10529400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:10520600-10529600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:10520600-10530200	Strong transcription	Fetal Intestine Small	intestine
36	chr1:10520600-10530400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:10521000-10529400	Strong transcription	Ovary	ovary
38	chr1:10521000-10529600	Strong transcription	Fetal Muscle Leg	muscle
39	chr1:10521000-10529600	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:10521000-10529600	Strong transcription	Dnd41	blood
41	chr1:10521000-10529800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr1:10521000-10530200	Strong transcription	Placenta	Placenta
43	chr1:10521200-10526400	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr1:10521200-10527000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:10521200-10527600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:10521200-10528400	Strong transcription	Liver	Liver
47	chr1:10521200-10529200	Strong transcription	Pancreas	Pancrea
48	chr1:10521200-10529400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:10521200-10529400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:10521200-10529400	Strong transcription	Duodenum Mucosa	Duodenum

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