Variant report

Variant	rs1059234
Chromosome Location	chr6:36653597-36653598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36650715..36656032-chr6:36664945..36667924,5	MCF-7	breast:
2	chr6:36581224..36597272-chr6:36642199..36659412,120	MCF-7	breast:
3	chr6:36645102..36656546-chr6:36717974..36730993,29	MCF-7	breast:
4	chr6:36645354..36650870-chr6:36653418..36656910,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAB44-3	chr6:36653528-36655108	NONHSAT112228

Variant related genes	Relation type
ENSG00000263894	Chromatin interaction
ENSG00000124772	Chromatin interaction
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10214861	1.00[CEU][hapmap]
rs10456441	0.80[JPT][hapmap]
rs10456442	0.80[JPT][hapmap]
rs10456443	0.80[JPT][hapmap]
rs11964420	1.00[CEU][hapmap]
rs11967202	1.00[CEU][hapmap]
rs12203953	0.80[JPT][hapmap]
rs12206430	0.85[JPT][hapmap]
rs12210094	0.80[JPT][hapmap]
rs12524435	0.80[JPT][hapmap]
rs12528248	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12530170	0.80[JPT][hapmap]
rs1801270	0.95[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs236378	1.00[CEU][hapmap]
rs3176345	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3176361	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3829963	0.85[JPT][hapmap]
rs4464789	0.80[JPT][hapmap]
rs4713993	0.80[JPT][hapmap]
rs4713998	0.83[MEX][hapmap]
rs4714005	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6457932	0.80[JPT][hapmap]
rs6916443	1.00[CEU][hapmap]
rs6920453	0.80[JPT][hapmap]
rs6931097	0.85[JPT][hapmap]
rs7747806	1.00[CEU][hapmap]
rs7757749	1.00[CEU][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7761648	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs876581	1.00[CEU][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9349002	0.85[JPT][hapmap]
rs9349005	0.85[JPT][hapmap]
rs9366912	0.80[JPT][hapmap]
rs9470400	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36649000-36654200	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:36649000-36654600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:36649400-36654200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:36649800-36654200	Genic enhancers	Adipose Nuclei	Adipose
5	chr6:36650400-36654400	Genic enhancers	Fetal Muscle Leg	muscle
6	chr6:36650400-36655200	Strong transcription	Aorta	Aorta
7	chr6:36650400-36656600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:36650600-36654600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:36650600-36655000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:36650600-36655600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:36650600-36655600	Strong transcription	HSMMtube	muscle
12	chr6:36650600-36655600	Strong transcription	NH-A	brain
13	chr6:36650800-36655000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:36650800-36655000	Weak transcription	K562	blood
15	chr6:36650800-36656000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:36650800-36659600	Weak transcription	Right Atrium	heart
17	chr6:36651000-36654800	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr6:36651000-36654800	Strong transcription	Rectal Smooth Muscle	rectum
19	chr6:36651000-36655200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:36651000-36655400	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:36651200-36654600	Strong transcription	Brain Cingulate Gyrus	brain
22	chr6:36651200-36654600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
23	chr6:36651200-36655200	Strong transcription	NHLF	lung
24	chr6:36651200-36655600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:36651200-36655600	Genic enhancers	Primary B cells from peripheral blood	blood
26	chr6:36651200-36655600	Strong transcription	Fetal Stomach	stomach
27	chr6:36651200-36655600	Strong transcription	HSMM	muscle
28	chr6:36651200-36655800	Strong transcription	NHDF-Ad	bronchial
29	chr6:36651200-36656000	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr6:36651200-36656200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:36651200-36660000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr6:36651400-36655000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr6:36651400-36655200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:36651400-36655200	Strong transcription	Colon Smooth Muscle	Colon
35	chr6:36651400-36655200	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:36651400-36655400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:36651600-36653600	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr6:36651600-36653800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr6:36651600-36654200	Strong transcription	Esophagus	oesophagus
40	chr6:36651600-36654800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:36651600-36655000	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr6:36651600-36655000	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr6:36651600-36655000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr6:36651600-36655000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:36651600-36655000	Strong transcription	Brain Anterior Caudate	brain
46	chr6:36651600-36655000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:36651600-36655000	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr6:36651600-36655000	Strong transcription	Small Intestine	intestine
49	chr6:36651600-36655200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr6:36651600-36655400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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