Variant report

Variant	rs9393593
Chromosome Location	chr6:24855751-24855752
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24855588..24857199-chr6:24871445..24874017,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1007237	0.90[MEX][hapmap]
rs2747670	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2747685	0.84[CEU][hapmap];0.85[MEX][hapmap]
rs4256430	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap]
rs62402002	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs926850	0.85[MEX][hapmap]
rs9366587	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9379697	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9393593	HIST1H3C	cis	cerebellum	SCAN
rs9393593	ALDH5A1	cis	lymphoblastoid	seeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24777000-24859600	Weak transcription	Psoas Muscle	Psoas
2	chr6:24804800-24858200	Weak transcription	Gastric	stomach
3	chr6:24817800-24855800	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr6:24818600-24855800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:24818800-24856000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr6:24818800-24856400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr6:24830400-24855800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:24832400-24859600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:24833000-24857800	Weak transcription	Brain Angular Gyrus	brain
10	chr6:24836000-24857200	Weak transcription	Fetal Brain Female	brain
11	chr6:24837000-24855800	Weak transcription	Ovary	ovary
12	chr6:24837800-24856000	Strong transcription	Fetal Thymus	thymus
13	chr6:24838000-24856400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:24838200-24856000	Strong transcription	Placenta	Placenta
15	chr6:24838200-24856400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:24838800-24855800	Weak transcription	Adipose Nuclei	Adipose
17	chr6:24839600-24858800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:24840400-24856400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:24842400-24856600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:24843000-24856000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:24843400-24855800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:24843400-24856000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:24843800-24858400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:24843800-24879400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:24844200-24859800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:24844600-24856600	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:24844600-24858200	Weak transcription	Right Ventricle	heart
28	chr6:24844600-24860200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:24844600-24873200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:24846000-24855800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:24846200-24858200	Weak transcription	Esophagus	oesophagus
32	chr6:24846200-24873400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:24846800-24866000	Weak transcription	Fetal Intestine Small	intestine
34	chr6:24847000-24876600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr6:24847800-24856600	Weak transcription	Lung	lung
36	chr6:24848400-24855800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr6:24848400-24857400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:24848400-24858200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:24848400-24860000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:24848600-24859600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr6:24849000-24855800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:24849000-24864600	Weak transcription	Brain Germinal Matrix	brain
43	chr6:24849200-24855800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr6:24849200-24855800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:24849200-24856200	Weak transcription	Brain Substantia Nigra	brain
46	chr6:24849200-24858200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr6:24850000-24858000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr6:24850400-24858800	Weak transcription	Liver	Liver
49	chr6:24850800-24856000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:24850800-24864600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links