Variant report

Variant	rs917077
Chromosome Location	chr7:39676036-39676037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39661695..39665595-chr7:39674627..39679140,4	MCF-7	breast:
2	chr7:39674562..39677134-chr7:39680609..39682142,2	K562	blood:
3	chr7:39670051..39673950-chr7:39675213..39677568,3	K562	blood:
4	chr7:39661719..39664605-chr7:39675748..39677342,2	MCF-7	breast:
5	chr7:39670051..39674974-chr7:39675213..39680609,7	K562	blood:

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11769865	0.87[EUR][1000 genomes]
rs11982634	0.85[EUR][1000 genomes]
rs2107710	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2158548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2158549	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2189837	0.88[EUR][1000 genomes]
rs2329464	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2876862	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3823742	0.88[EUR][1000 genomes]
rs4723887	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723891	0.88[EUR][1000 genomes]
rs4723892	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6462936	0.83[EUR][1000 genomes]
rs6462937	0.92[EUR][1000 genomes]
rs6952363	0.88[EUR][1000 genomes]
rs6952866	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6956681	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6961667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969070	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6969523	0.91[EUR][1000 genomes]
rs7785049	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806651	0.88[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	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv887972	chr7:39666267-39733688	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs917077	LINC00265	cis	lung	GTEx
rs917077	LINC00265	cis	Thyroid	GTEx
rs917077	LINC00265	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39664400-39678400	Weak transcription	Placenta	Placenta
2	chr7:39664400-39679600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:39665200-39677800	Weak transcription	Brain Substantia Nigra	brain
4	chr7:39665400-39679800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr7:39665600-39680400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:39665600-39682200	Weak transcription	Liver	Liver
7	chr7:39666200-39678200	Weak transcription	Brain Germinal Matrix	brain
8	chr7:39666200-39679000	Weak transcription	Esophagus	oesophagus
9	chr7:39666200-39681800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:39666200-39694400	Weak transcription	Fetal Brain Female	brain
11	chr7:39666800-39681200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:39667200-39698800	Weak transcription	Fetal Kidney	kidney
13	chr7:39667600-39678800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:39668200-39681000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:39668200-39681000	Weak transcription	Fetal Heart	heart
16	chr7:39668600-39680600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:39669600-39681200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:39671200-39677400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr7:39671800-39676600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr7:39671800-39677400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:39671800-39679600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:39671800-39679800	Weak transcription	Ovary	ovary
23	chr7:39671800-39693800	Weak transcription	A549	lung
24	chr7:39672200-39679200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:39672200-39679200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr7:39672200-39679400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:39672200-39681600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr7:39672200-39681800	Weak transcription	Gastric	stomach
29	chr7:39672200-39681800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr7:39672200-39684000	Weak transcription	NHLF	lung
31	chr7:39672200-39722800	Weak transcription	Hela-S3	cervix
32	chr7:39672400-39683200	Weak transcription	Pancreas	Pancrea
33	chr7:39672800-39679600	Weak transcription	Aorta	Aorta
34	chr7:39672800-39680400	Weak transcription	K562	blood
35	chr7:39672800-39681800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr7:39673400-39677600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:39673400-39679600	Weak transcription	Brain Angular Gyrus	brain
38	chr7:39673600-39678400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:39673600-39679000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr7:39673600-39679400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr7:39673800-39676400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr7:39673800-39676400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr7:39673800-39676600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr7:39674000-39676200	Weak transcription	Osteobl	bone
45	chr7:39674000-39678200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:39674000-39678200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr7:39674000-39678200	Weak transcription	Left Ventricle	heart
48	chr7:39674000-39678400	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr7:39674000-39678400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr7:39674000-39679000	Weak transcription	Adipose Nuclei	Adipose

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