Variant report

Variant	rs325001
Chromosome Location	chr6:44270936-44270937
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:44270681-44271130	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:44270705-44271176	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:44221494..44225979-chr6:44269650..44274771,6	K562	blood:
2	chr6:44252510..44254427-chr6:44270655..44272831,2	MCF-7	breast:
3	chr6:44094457..44097245-chr6:44270465..44272999,2	K562	blood:
4	chr6:44213299..44216188-chr6:44269950..44273084,4	K562	blood:
5	chr6:44244057..44246531-chr6:44270330..44272647,2	MCF-7	breast:

No data

Variant related genes	Relation type
AARS2	TF binding region
ENSG00000180992	Chromatin interaction
ENSG00000137216	Chromatin interaction
ENSG00000265700	Chromatin interaction
ENSG00000157593	Chromatin interaction
ENSG00000096384	Chromatin interaction
ENSG00000146221	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12215017	0.94[ASN][1000 genomes]
rs167772	0.92[CEU][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2233437	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs324137	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs325000	0.81[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs325002	0.98[ASN][1000 genomes]
rs325004	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3799962	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs3818685	0.89[CEU][hapmap];0.86[CHD][hapmap];0.85[EUR][1000 genomes]
rs483536	0.86[JPT][hapmap]
rs498512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs513688	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs639728	0.93[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs651297	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs730775	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs7772949	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv462936	chr6:44191920-44282316	Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv603004	chr6:44191920-44282316	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv885853	chr6:44197181-44274797	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv885854	chr6:44211867-44274797	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv462937	chr6:44211867-44279111	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
7	nsv603005	chr6:44211867-44279111	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
8	esv1807818	chr6:44266574-44275011	Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs325001	TCTE1	cis	cerebellum	SCAN
rs325001	TCTE1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44265600-44279600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:44266000-44271600	Weak transcription	NHDF-Ad	bronchial
3	chr6:44266000-44272400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr6:44266000-44276600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:44266000-44277000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr6:44266000-44280000	Weak transcription	Small Intestine	intestine
7	chr6:44266200-44271200	Weak transcription	Fetal Brain Male	brain
8	chr6:44266200-44276400	Weak transcription	Fetal Heart	heart
9	chr6:44266200-44276800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:44266200-44279600	Weak transcription	Right Atrium	heart
11	chr6:44266800-44272400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:44266800-44273600	Strong transcription	Fetal Stomach	stomach
13	chr6:44266800-44276600	Strong transcription	Fetal Intestine Small	intestine
14	chr6:44266800-44279200	Strong transcription	Brain Cingulate Gyrus	brain
15	chr6:44266800-44279800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:44267000-44272800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:44267000-44275400	Weak transcription	Fetal Kidney	kidney
18	chr6:44267000-44276600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:44267000-44279600	Strong transcription	Fetal Muscle Leg	muscle
20	chr6:44267000-44279800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:44267000-44279800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr6:44267200-44279400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:44267200-44279600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr6:44267200-44279600	Strong transcription	Fetal Thymus	thymus
25	chr6:44267200-44279800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:44267200-44279800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:44267400-44272800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr6:44267400-44275400	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:44267400-44275600	Strong transcription	NHLF	lung
30	chr6:44267400-44276400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:44267400-44276600	Strong transcription	NHEK	skin
32	chr6:44267400-44276800	Strong transcription	Fetal Intestine Large	intestine
33	chr6:44267400-44279200	Strong transcription	Liver	Liver
34	chr6:44267400-44279400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:44267400-44279600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:44267400-44279600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:44267400-44280000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:44267400-44280000	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr6:44267600-44279200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr6:44267600-44279400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr6:44267600-44279800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:44267800-44274400	Strong transcription	Brain Substantia Nigra	brain
43	chr6:44267800-44276600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:44267800-44277000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr6:44267800-44279800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:44267800-44279800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr6:44268000-44271200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:44268000-44271800	Strong transcription	Primary hematopoietic stem cells	blood
49	chr6:44268000-44272200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:44268000-44272400	Strong transcription	H1 Cell Line	embryonic stem cell

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