Variant report

Variant	rs17080460
Chromosome Location	chr6:149274114-149274115
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:149274093-149274224	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149067550..149069400-chr6:149273636..149276626,2	MCF-7	breast:

Variant related genes	Relation type
UST	TF binding region
ENSG00000111962	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10499255	0.88[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12175861	0.83[AMR][1000 genomes]
rs1320576	1.00[EUR][1000 genomes]
rs17079955	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080135	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56252829	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59303380	1.00[EUR][1000 genomes]
rs60626199	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73778945	1.00[EUR][1000 genomes]
rs73778952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73778957	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73778960	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73778961	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73778963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73778964	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73778968	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73778969	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7741642	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149256600-149292600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:149257000-149285000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:149257600-149276200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:149261400-149285000	Weak transcription	Spleen	Spleen
5	chr6:149262000-149289600	Weak transcription	Aorta	Aorta
6	chr6:149262200-149276200	Weak transcription	Pancreas	Pancrea
7	chr6:149263400-149275400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:149263400-149275600	Weak transcription	Primary B cells from cord blood	blood
9	chr6:149263400-149275600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr6:149263400-149275600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:149266800-149276200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr6:149267000-149276400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:149269200-149276600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:149269400-149276000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:149269400-149277600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:149269400-149288800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:149269400-149291400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:149269600-149275800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:149269600-149276400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:149269600-149277800	Weak transcription	Brain Substantia Nigra	brain
21	chr6:149270600-149274200	Enhancers	Rectal Smooth Muscle	rectum
22	chr6:149271200-149275600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:149271200-149276600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:149271200-149288600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:149271400-149275600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:149271400-149276000	Weak transcription	Right Atrium	heart
27	chr6:149271600-149275600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:149271600-149276000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr6:149271600-149276000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:149271600-149277600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:149271600-149285600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:149271800-149275400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr6:149271800-149275600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:149271800-149276000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:149272400-149274200	Enhancers	Ovary	ovary
36	chr6:149272600-149274600	Enhancers	Fetal Lung	lung
37	chr6:149272800-149283400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:149273000-149274600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:149273000-149274600	Enhancers	Colon Smooth Muscle	Colon
40	chr6:149273200-149274200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:149273200-149274200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:149273200-149274200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr6:149273200-149274400	Enhancers	Fetal Kidney	kidney
44	chr6:149273200-149274400	Enhancers	Fetal Stomach	stomach
45	chr6:149273400-149274400	Enhancers	NHLF	lung
46	chr6:149273600-149274200	Enhancers	Muscle Satellite Cultured Cells	--
47	chr6:149273600-149275800	Weak transcription	Fetal Intestine Small	intestine
48	chr6:149273800-149274600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:149273800-149276200	Weak transcription	Stomach Mucosa	stomach
50	chr6:149274000-149274600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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