Variant report

Variant	rs17496254
Chromosome Location	chr7:40016449-40016450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39986728..39990828-chr7:40016183..40019996,4	MCF-7	breast:
2	chr7:40016185..40017725-chr7:40028366..40031128,2	K562	blood:
3	chr7:39988178..39991178-chr7:40012997..40016738,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065883	Chromatin interaction
ENSG00000259826	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17171650	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17171651	0.84[AFR][1000 genomes]
rs17496240	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17537775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17537887	1.00[EUR][1000 genomes]
rs17537936	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17537957	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17538034	1.00[EUR][1000 genomes]
rs17538139	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17538293	1.00[EUR][1000 genomes]
rs1973397	1.00[EUR][1000 genomes]
rs57602515	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57832352	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57938128	1.00[EUR][1000 genomes]
rs60166394	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60489461	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6952564	1.00[EUR][1000 genomes]
rs6975868	1.00[EUR][1000 genomes]
rs6977290	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7781392	0.91[AFR][1000 genomes]
rs7797651	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7797841	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7803136	0.93[AFR][1000 genomes]
rs7809041	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv887976	chr7:39874986-40018693	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv887977	chr7:39885541-40018693	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv1015322	chr7:40006195-40141195	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	esv2761319	chr7:40006195-40142139	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39993600-40048200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:39994200-40027200	Weak transcription	HSMM	muscle
3	chr7:39994800-40018000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:39995000-40018200	Weak transcription	Spleen	Spleen
5	chr7:39995200-40042600	Weak transcription	K562	blood
6	chr7:39996800-40016600	Weak transcription	Gastric	stomach
7	chr7:39997800-40027400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr7:39998000-40027200	Weak transcription	Hela-S3	cervix
9	chr7:40000400-40016600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr7:40001000-40016600	Weak transcription	Dnd41	blood
11	chr7:40001000-40018600	Weak transcription	Thymus	Thymus
12	chr7:40001200-40016800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:40001200-40018200	Weak transcription	Fetal Thymus	thymus
14	chr7:40005600-40021000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr7:40005600-40021000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr7:40006600-40018200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr7:40006600-40019800	Enhancers	Primary B cells from peripheral blood	blood
18	chr7:40006800-40031200	Weak transcription	Fetal Stomach	stomach
19	chr7:40007200-40017400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr7:40007200-40027200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr7:40007600-40027200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:40008200-40016800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr7:40008800-40018200	Weak transcription	Right Atrium	heart
24	chr7:40009000-40016800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr7:40009400-40020800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr7:40009400-40027200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr7:40009400-40027400	Weak transcription	Osteobl	bone
28	chr7:40009600-40016600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr7:40009600-40016600	Weak transcription	Brain Substantia Nigra	brain
30	chr7:40009600-40018000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:40009600-40027400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:40009800-40027200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:40010000-40024600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:40010000-40026800	Weak transcription	NHEK	skin
35	chr7:40010200-40025000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr7:40010400-40027200	Weak transcription	Esophagus	oesophagus
37	chr7:40011000-40021000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr7:40011200-40016600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr7:40011200-40023600	Weak transcription	Lung	lung
40	chr7:40011200-40025400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr7:40011400-40027400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr7:40011800-40016600	Weak transcription	Colon Smooth Muscle	Colon
43	chr7:40012200-40016800	Weak transcription	Brain Anterior Caudate	brain
44	chr7:40012200-40017000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr7:40012200-40017800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr7:40012200-40018000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr7:40012400-40017800	Weak transcription	Adipose Nuclei	Adipose
48	chr7:40012600-40016600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr7:40012600-40016800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr7:40014000-40017200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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