Variant report

Variant	rs55858240
Chromosome Location	chr6:150047899-150047900
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:150045566..150048616-chr6:150051147..150053012,3	K562	blood:
2	chr6:150039916..150042698-chr6:150047893..150050444,2	MCF-7	breast:
3	chr6:150037459..150041467-chr6:150046998..150054266,14	K562	blood:
4	chr6:149967346..149970851-chr6:150047639..150051197,3	K562	blood:
5	chr6:150045603..150048422-chr6:150052739..150054245,2	MCF-7	breast:
6	chr6:150043756..150046573-chr6:150046900..150049362,3	K562	blood:
7	chr6:150043754..150045572-chr6:150046900..150050197,3	K562	blood:

Variant related genes	Relation type
ENSG00000186625	Chromatin interaction
ENSG00000131023	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17710991	1.00[ASN][1000 genomes]
rs62439707	1.00[ASN][1000 genomes]
rs62439751	1.00[ASN][1000 genomes]
rs62439806	1.00[ASN][1000 genomes]
rs62439846	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886762	chr6:149866452-150174507	Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1792620	chr6:149909491-150083621	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	esv3475167	chr6:150003006-150086225	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv3475168	chr6:150003006-150086225	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	esv1803291	chr6:150018508-150164190	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55858240	C6orf72	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150039600-150049600	Weak transcription	Spleen	Spleen
2	chr6:150039600-150049800	Weak transcription	Gastric	stomach
3	chr6:150039600-150050400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:150039800-150049800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:150039800-150049800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:150039800-150066800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:150039800-150067000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:150040000-150049000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:150040000-150049000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr6:150040000-150049000	Weak transcription	Right Ventricle	heart
11	chr6:150040000-150049400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:150040000-150049400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:150040000-150049600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:150040000-150049600	Weak transcription	Brain Substantia Nigra	brain
15	chr6:150040000-150049800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:150040000-150049800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:150040000-150049800	Weak transcription	Aorta	Aorta
18	chr6:150040000-150049800	Weak transcription	Brain Angular Gyrus	brain
19	chr6:150040000-150049800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr6:150040000-150049800	Weak transcription	Fetal Lung	lung
21	chr6:150040000-150049800	Weak transcription	Pancreas	Pancrea
22	chr6:150040000-150050000	Weak transcription	Esophagus	oesophagus
23	chr6:150040000-150050400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:150040000-150050400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:150040000-150050400	Weak transcription	Lung	lung
26	chr6:150040000-150051800	Weak transcription	Small Intestine	intestine
27	chr6:150040000-150056400	Weak transcription	Psoas Muscle	Psoas
28	chr6:150040000-150057400	Weak transcription	A549	lung
29	chr6:150040000-150066600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr6:150040200-150048000	Weak transcription	Osteobl	bone
31	chr6:150040200-150048400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:150040200-150049000	Weak transcription	Fetal Kidney	kidney
33	chr6:150040200-150049200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:150040200-150049200	Weak transcription	Brain Hippocampus Middle	brain
35	chr6:150040200-150049400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:150040200-150049400	Weak transcription	Brain Germinal Matrix	brain
37	chr6:150040200-150049600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr6:150040200-150049600	Weak transcription	Thymus	Thymus
39	chr6:150040200-150049600	Weak transcription	Hela-S3	cervix
40	chr6:150040200-150049800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:150040200-150056200	Weak transcription	Colonic Mucosa	Colon
42	chr6:150040400-150066200	Weak transcription	Fetal Brain Male	brain
43	chr6:150040600-150049000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:150040600-150049600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:150043600-150065600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:150043600-150066000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:150043800-150049400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr6:150043800-150053800	Strong transcription	Dnd41	blood
49	chr6:150043800-150064000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:150044000-150048400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links