Variant report

Variant	rs7743396
Chromosome Location	chr6:36579252-36579253
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36577655..36580649-chr6:36645299..36647477,2	MCF-7	breast:
2	chr6:36577436..36580901-chr6:36648470..36651354,3	K562	blood:
3	chr6:36578752..36581618-chr6:36589412..36591182,2	K562	blood:
4	chr6:36576949..36579630-chr6:36689690..36691532,2	K562	blood:
5	chr6:36539071..36541420-chr6:36578039..36580553,2	K562	blood:
6	chr6:36577411..36580093-chr6:36598443..36601341,2	K562	blood:
7	chr6:36578336..36580257-chr6:36585144..36586920,2	MCF-7	breast:
8	chr6:36577490..36580113-chr6:36675769..36678702,3	K562	blood:
9	chr6:36578466..36580870-chr6:36647924..36649824,2	MCF-7	breast:
10	chr6:36574853..36581451-chr6:36644915..36649997,7	K562	blood:
11	chr6:36577343..36580259-chr6:36718203..36721182,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000263894	Chromatin interaction
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10214849	0.81[CHD][hapmap]
rs1061632	0.81[CEU][hapmap]
rs1076931	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10807169	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947613	0.94[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.80[ASN][1000 genomes]
rs10947614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11755264	0.81[CEU][hapmap]
rs11756557	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11756969	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap]
rs11757842	0.81[CEU][hapmap]
rs1191	0.81[CEU][hapmap]
rs12153820	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12190062	0.81[CEU][hapmap]
rs12202732	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12208086	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12211825	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1535510	0.81[CEU][hapmap]
rs16888552	0.81[CEU][hapmap]
rs1812018	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1812019	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1812020	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1983781	0.81[CEU][hapmap]
rs2001101	0.97[EUR][1000 genomes]
rs2007741	0.81[CEU][hapmap]
rs2145048	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2146333	0.80[CEU][hapmap]
rs2180929	0.81[CEU][hapmap]
rs2187827	0.81[CEU][hapmap]
rs2239807	0.81[CEU][hapmap]
rs2239808	0.81[CEU][hapmap]
rs2300064	0.81[CEU][hapmap]
rs3798473	0.81[CEU][hapmap]
rs3819760	0.81[CEU][hapmap]
rs4598	0.81[CEU][hapmap]
rs4713973	0.88[CEU][hapmap]
rs56144242	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61211228	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6457920	0.81[CEU][hapmap]
rs6457923	0.81[CEU][hapmap]
rs6457928	0.81[CEU][hapmap]
rs6457929	0.81[CEU][hapmap]
rs6899372	0.80[CEU][hapmap]
rs6905347	0.81[CEU][hapmap]
rs6905686	0.81[CEU][hapmap]
rs6911877	0.81[CEU][hapmap]
rs6912117	0.81[CEU][hapmap]
rs6912982	0.81[CEU][hapmap]
rs6913530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6913613	0.81[CEU][hapmap]
rs6913714	0.81[CEU][hapmap]
rs6917951	0.80[CEU][hapmap]
rs6920166	0.81[CEU][hapmap]
rs6926522	0.81[CEU][hapmap]
rs6927896	0.81[CEU][hapmap]
rs6928087	0.80[CEU][hapmap]
rs6936942	0.81[CEU][hapmap]
rs6941593	0.81[CEU][hapmap]
rs72852338	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72852340	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7344	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741888	0.83[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7747264	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7755461	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7759778	0.83[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7759933	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7760766	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7767296	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7772524	0.81[CEU][hapmap]
rs9296193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs933236	0.81[CEU][hapmap]
rs9349001	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357217	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9357218	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9357219	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9366907	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9366908	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9366909	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9368938	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9368939	0.94[EUR][1000 genomes]
rs9368940	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9368943	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380577	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9380578	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9380580	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9380582	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9394359	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9394360	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9394361	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9394362	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9394363	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9394365	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9470280	0.81[CEU][hapmap]
rs9470294	0.81[CEU][hapmap]
rs9470295	0.81[CEU][hapmap]
rs9470297	0.81[CEU][hapmap]
rs9470300	0.81[CEU][hapmap]
rs9470302	0.80[CEU][hapmap]

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	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7743396	GLO1	cis	cerebellum	SCAN
rs7743396	TULP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36566800-36582800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:36567000-36580400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:36568000-36581400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr6:36568200-36580200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:36568600-36584600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:36568800-36581200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:36569000-36581600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:36569400-36581600	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:36569600-36581400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:36569600-36585000	Strong transcription	Fetal Thymus	thymus
11	chr6:36570000-36581800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr6:36570200-36581200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr6:36570400-36581600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:36570400-36584800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:36570600-36582000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:36570800-36580200	Strong transcription	NH-A	brain
17	chr6:36571000-36581600	Strong transcription	Primary B cells from cord blood	blood
18	chr6:36571200-36581600	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr6:36571200-36582200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:36571600-36585000	Strong transcription	Thymus	Thymus
21	chr6:36571800-36582200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:36572000-36579400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:36572000-36581800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:36572000-36583200	Strong transcription	Fetal Stomach	stomach
25	chr6:36572600-36580400	Strong transcription	HUVEC	blood vessel
26	chr6:36572600-36581400	Strong transcription	Dnd41	blood
27	chr6:36572600-36582200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:36573200-36581200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:36573600-36582800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:36574000-36581600	Strong transcription	Brain Germinal Matrix	brain
31	chr6:36574200-36580200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:36574200-36580400	Strong transcription	HSMM	muscle
33	chr6:36574600-36580000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:36574600-36581200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:36575200-36580000	Strong transcription	Primary hematopoietic stem cells	blood
36	chr6:36575200-36580400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:36575400-36581600	Strong transcription	Fetal Muscle Trunk	muscle
38	chr6:36575600-36580000	Strong transcription	NHDF-Ad	bronchial
39	chr6:36575600-36583200	Weak transcription	Hela-S3	cervix
40	chr6:36576000-36579800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:36576000-36580200	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr6:36576000-36580400	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr6:36576000-36580400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:36576000-36580800	Weak transcription	Fetal Brain Male	brain
45	chr6:36576000-36581000	Strong transcription	Osteobl	bone
46	chr6:36576000-36581400	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:36576000-36581400	Strong transcription	Primary T cells from cord blood	blood
48	chr6:36576000-36581600	Strong transcription	Fetal Lung	lung
49	chr6:36576000-36581800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:36576200-36579800	Weak transcription	Brain Angular Gyrus	brain

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