Variant report

Variant	rs3817742
Chromosome Location	chr6:13279552-13279553
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	chr6:13266277..13270174-chr6:13278637..13282022,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GFOD1-1	chr6:13279527-13281388	ENSG00000215022.3

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1223397	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1223399	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1223400	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1223401	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1223402	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1223403	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1232392	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13191897	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13205692	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17700321	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17767967	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs202016	0.80[ASN][1000 genomes]
rs202017	0.80[ASN][1000 genomes]
rs202018	0.80[ASN][1000 genomes]
rs202019	0.80[ASN][1000 genomes]
rs202021	0.80[ASN][1000 genomes]
rs202023	0.80[ASN][1000 genomes]
rs2048552	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs20499	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs20500	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2439534	0.80[ASN][1000 genomes]
rs2439535	0.80[ASN][1000 genomes]
rs2439537	0.80[ASN][1000 genomes]
rs2439539	0.80[ASN][1000 genomes]
rs2439541	0.80[ASN][1000 genomes]
rs2439542	0.80[ASN][1000 genomes]
rs2439545	0.80[ASN][1000 genomes]
rs2439548	0.80[ASN][1000 genomes]
rs2439549	0.80[ASN][1000 genomes]
rs2458309	0.80[ASN][1000 genomes]
rs2458310	0.80[ASN][1000 genomes]
rs2458311	0.80[ASN][1000 genomes]
rs2458312	0.80[ASN][1000 genomes]
rs2496140	0.80[ASN][1000 genomes]
rs2496142	0.80[ASN][1000 genomes]
rs2496144	0.80[ASN][1000 genomes]
rs2496145	0.80[ASN][1000 genomes]
rs2496147	0.80[ASN][1000 genomes]
rs2496148	0.80[ASN][1000 genomes]
rs2496149	0.80[ASN][1000 genomes]
rs2496151	0.80[ASN][1000 genomes]
rs2496152	0.80[ASN][1000 genomes]
rs2496153	0.80[ASN][1000 genomes]
rs2496154	0.80[ASN][1000 genomes]
rs2496156	0.80[ASN][1000 genomes]
rs2919685	0.80[ASN][1000 genomes]
rs2919686	0.80[ASN][1000 genomes]
rs3001966	0.80[ASN][1000 genomes]
rs3001967	0.80[ASN][1000 genomes]
rs34505804	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35511719	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35549743	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3734878	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3817737	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817738	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3817741	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402705	0.81[ASN][1000 genomes]
rs449727	0.81[ASN][1000 genomes]
rs452309	0.80[ASN][1000 genomes]
rs453877	0.80[ASN][1000 genomes]
rs9349564	0.80[ASN][1000 genomes]
rs9357660	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9381884	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395602	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957175	0.80[ASN][1000 genomes]
rs957176	0.80[ASN][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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS 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	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
2	chr6:13267400-13280400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:13267400-13283600	Weak transcription	Fetal Brain Female	brain
4	chr6:13268000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:13269200-13282000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:13269400-13284800	Weak transcription	Right Atrium	heart
7	chr6:13269600-13286600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:13269600-13286600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr6:13270200-13291600	Weak transcription	HSMM	muscle
10	chr6:13270400-13282000	Weak transcription	Ovary	ovary
11	chr6:13270400-13285400	Weak transcription	Fetal Heart	heart
12	chr6:13270600-13281000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:13270600-13283600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:13271600-13287200	Weak transcription	Fetal Lung	lung
15	chr6:13273000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:13273400-13286800	Weak transcription	Liver	Liver
17	chr6:13273800-13280400	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:13273800-13291400	Weak transcription	Psoas Muscle	Psoas
19	chr6:13274000-13282600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:13274000-13283800	Weak transcription	Brain Substantia Nigra	brain
21	chr6:13274400-13286800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:13274400-13287200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:13274400-13289200	Weak transcription	HSMMtube	muscle
24	chr6:13274600-13286200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:13274600-13286800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
27	chr6:13274800-13286600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr6:13274800-13287000	Weak transcription	Thymus	Thymus
29	chr6:13274800-13292800	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:13275000-13280400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr6:13275000-13282800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:13275000-13285000	Weak transcription	Fetal Intestine Small	intestine
33	chr6:13275000-13286800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:13275000-13287000	Weak transcription	Gastric	stomach
35	chr6:13275200-13280200	Weak transcription	Primary T cells from cord blood	blood
36	chr6:13275200-13286400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:13275600-13280200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:13275600-13281000	Weak transcription	Placenta	Placenta
39	chr6:13275600-13286600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr6:13275600-13287000	Weak transcription	Adipose Nuclei	Adipose
41	chr6:13275600-13291600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr6:13275800-13282200	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:13276000-13279800	Weak transcription	Spleen	Spleen
44	chr6:13276000-13282800	Weak transcription	Right Ventricle	heart
45	chr6:13276000-13287400	Genic enhancers	Primary B cells from peripheral blood	blood
46	chr6:13276200-13279600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr6:13276200-13281400	Genic enhancers	Primary B cells from cord blood	blood
48	chr6:13276600-13281000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:13277200-13281600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:13277200-13282000	Strong transcription	Left Ventricle	heart

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