Variant report

Variant	rs56344861
Chromosome Location	chr6:24717056-24717057
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24711892..24724164-chr6:24769415..24786834,81	K562	blood:
2	chr6:24715365..24725462-chr6:24770390..24783002,86	K562	blood:
3	chr6:24716219..24722234-chr6:24748111..24753033,8	K562	blood:
4	chr6:24714616..24717353-chr6:24764940..24766713,2	K562	blood:
5	chr6:24696748..24707740-chr6:24716503..24724189,24	MCF-7	breast:
6	chr6:24656525..24658806-chr6:24716394..24719369,2	K562	blood:
7	chr6:24661385..24670379-chr6:24713871..24722680,32	K562	blood:
8	chr6:24670678..24672473-chr6:24716223..24718706,2	K562	blood:
9	chr6:24717012..24718789-chr6:24741249..24744082,2	MCF-7	breast:
10	chr6:24586729..24589298-chr6:24716794..24718796,2	K562	blood:
11	chr6:24660920..24672880-chr6:24713381..24723000,42	K562	blood:
12	chr6:24654228..24658025-chr6:24716632..24719423,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272402	Chromatin interaction
ENSG00000224164	Chromatin interaction
ENSG00000218806	Chromatin interaction
ENSG00000112312	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000272345	Chromatin interaction
ENSG00000111802	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11753290	0.81[EUR][1000 genomes]
rs17249505	0.81[EUR][1000 genomes]
rs3181228	0.81[EUR][1000 genomes]
rs4544900	0.82[EUR][1000 genomes]
rs6456632	0.80[EUR][1000 genomes]
rs6909099	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6927947	0.88[EUR][1000 genomes]
rs6928668	0.82[EUR][1000 genomes]
rs6931809	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7757919	0.89[EUR][1000 genomes]
rs7765904	0.88[EUR][1000 genomes]
rs9356943	0.90[EUR][1000 genomes]
rs9358791	0.82[EUR][1000 genomes]
rs9366580	0.90[EUR][1000 genomes]
rs9379685	0.90[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	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
4	nsv428474	chr6:24714157-24797977	Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers 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	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56344861	C6orf62	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24698200-24717400	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr6:24698400-24717400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
3	chr6:24699000-24717400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:24703000-24717200	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr6:24703800-24718000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:24705000-24717400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:24708800-24719400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:24709600-24719000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:24709800-24717600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:24712000-24717200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:24712400-24717800	Genic enhancers	Brain Substantia Nigra	brain
12	chr6:24712600-24717600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr6:24712800-24719600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
14	chr6:24713000-24717400	Genic enhancers	Primary B cells from cord blood	blood
15	chr6:24713200-24717400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
16	chr6:24714200-24717600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:24714200-24717600	Genic enhancers	Primary monocytes fromperipheralblood	blood
18	chr6:24714800-24717400	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr6:24714800-24717600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:24714800-24717800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
21	chr6:24714800-24719000	Genic enhancers	Primary B cells from peripheral blood	blood
22	chr6:24715000-24718600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:24715000-24719600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:24715200-24718000	Enhancers	Fetal Heart	heart
25	chr6:24715200-24719600	Weak transcription	Spleen	Spleen
26	chr6:24715200-24720000	Transcr. at gene 5' and 3'	Dnd41	blood
27	chr6:24715400-24717400	Genic enhancers	Rectal Mucosa Donor 31	rectum
28	chr6:24715800-24717200	Transcr. at gene 5' and 3'	Psoas Muscle	Psoas
29	chr6:24715800-24717600	Genic enhancers	Fetal Thymus	thymus
30	chr6:24716000-24718400	Weak transcription	Lung	lung
31	chr6:24716000-24719200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:24716200-24717200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr6:24716200-24717200	Genic enhancers	Fetal Intestine Large	intestine
34	chr6:24716200-24717200	Genic enhancers	NHEK	skin
35	chr6:24716200-24717400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
36	chr6:24716200-24717400	Genic enhancers	Fetal Intestine Small	intestine
37	chr6:24716200-24717600	Genic enhancers	HSMM	muscle
38	chr6:24716200-24718400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr6:24716200-24718400	Transcr. at gene 5' and 3'	Hela-S3	cervix
40	chr6:24716200-24719000	Transcr. at gene 5' and 3'	Osteobl	bone
41	chr6:24716200-24719400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
42	chr6:24716200-24719600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:24716200-24719600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
44	chr6:24716400-24717200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
45	chr6:24716400-24717200	Genic enhancers	Fetal Stomach	stomach
46	chr6:24716400-24717400	Genic enhancers	Fetal Lung	lung
47	chr6:24716400-24717600	Enhancers	Brain Cingulate Gyrus	brain
48	chr6:24716400-24717800	Enhancers	Gastric	stomach
49	chr6:24716400-24718400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr6:24716400-24719600	Weak transcription	Esophagus	oesophagus

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