Variant report

Variant	rs793680
Chromosome Location	chr6:24428903-24428904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24421995..24424017-chr6:24428873..24431634,2	K562	blood:
2	chr6:24426316..24427953-chr6:24428203..24431025,2	MCF-7	breast:
3	chr6:24423442..24426628-chr6:24427479..24429179,4	MCF-7	breast:
4	chr6:24424515..24426613-chr6:24427739..24429764,2	K562	blood:
5	chr6:24426425..24428903-chr6:24718888..24721058,2	MCF-7	breast:
6	chr6:24402229..24405454-chr6:24428896..24431433,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124532	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1056283	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.88[TSI][hapmap];0.95[ASN][1000 genomes]
rs1277343	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1321819	0.94[ASN][1000 genomes]
rs13735	0.89[CHB][hapmap];0.97[CHD][hapmap];0.92[ASN][1000 genomes]
rs1742280	0.81[ASN][1000 genomes]
rs1742282	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1772253	0.90[CHD][hapmap]
rs2793422	0.86[CHD][hapmap]
rs3827640	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.92[ASN][1000 genomes]
rs6456612	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6920147	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6936856	0.82[ASN][1000 genomes]
rs7769012	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs793652	0.85[ASN][1000 genomes]
rs793654	0.90[CHD][hapmap]
rs793682	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793684	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793686	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs793687	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs793688	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs793690	0.81[ASN][1000 genomes]
rs9393554	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs793680	MRS2	cis	cerebellum	SCAN
rs793680	MRS2L	Cis_1M	lymphoblastoid	RTeQTL
rs793680	MRS2	cis	Esophagus Muscularis	GTEx
rs793680	MRS2	cis	Whole Blood	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24404600-24437400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:24410000-24430800	Strong transcription	Left Ventricle	heart
3	chr6:24412600-24429000	Strong transcription	Primary B cells from cord blood	blood
4	chr6:24412600-24430800	Strong transcription	Primary T cells from cord blood	blood
5	chr6:24413400-24429600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:24417400-24451800	Strong transcription	Liver	Liver
7	chr6:24420600-24429000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:24421200-24429000	Weak transcription	NHLF	lung
9	chr6:24421200-24448800	Weak transcription	Gastric	stomach
10	chr6:24421200-24459600	Weak transcription	Spleen	Spleen
11	chr6:24421400-24434000	Weak transcription	Fetal Brain Male	brain
12	chr6:24421600-24432000	Weak transcription	Fetal Heart	heart
13	chr6:24422400-24429400	Strong transcription	Brain Anterior Caudate	brain
14	chr6:24422400-24431400	Weak transcription	Fetal Intestine Small	intestine
15	chr6:24422400-24437400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:24423400-24429000	Weak transcription	Fetal Stomach	stomach
17	chr6:24423400-24433600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:24423400-24437200	Weak transcription	Pancreas	Pancrea
19	chr6:24423400-24439400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:24423600-24437200	Weak transcription	Right Ventricle	heart
21	chr6:24423800-24432000	Weak transcription	NHEK	skin
22	chr6:24424000-24432200	Weak transcription	Small Intestine	intestine
23	chr6:24424000-24456600	Weak transcription	Ovary	ovary
24	chr6:24424400-24445800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr6:24425000-24429200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:24425400-24432000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:24425400-24437200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:24425400-24439600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:24425600-24429200	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:24425600-24429400	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:24426000-24431000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:24426000-24438800	Weak transcription	Brain Substantia Nigra	brain
33	chr6:24426200-24430600	Weak transcription	Esophagus	oesophagus
34	chr6:24426200-24431600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:24426200-24446000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:24426400-24429600	Strong transcription	Fetal Muscle Leg	muscle
37	chr6:24426400-24431400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr6:24426400-24432400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr6:24426400-24441600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr6:24426400-24446000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:24426600-24438800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr6:24427000-24431600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr6:24427200-24429000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr6:24427200-24429000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:24427200-24433800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:24427400-24435000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:24427600-24429000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:24427600-24429000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr6:24427600-24429000	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr6:24427600-24432400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links