Variant report

Variant	rs6704234
Chromosome Location	chr1:212573298-212573299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212572555..212575344-chr1:212781722..212783615,2	K562	blood:

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11803766	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12239580	0.81[AFR][1000 genomes]
rs12739715	0.98[EUR][1000 genomes]
rs12755383	0.99[EUR][1000 genomes]
rs17018997	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2166155	0.83[AFR][1000 genomes]
rs35702733	0.98[EUR][1000 genomes]
rs35822123	0.82[EUR][1000 genomes]
rs4336916	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4540733	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4548507	0.83[AFR][1000 genomes]
rs6666415	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6669027	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6676208	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6693849	0.81[EUR][1000 genomes]
rs6697910	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71646158	0.82[EUR][1000 genomes]
rs71646159	0.93[EUR][1000 genomes]
rs71646161	0.99[EUR][1000 genomes]
rs7533689	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7551910	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
6	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6704234	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx
rs6704234	RP11-15I11.3	cis	Thyroid	GTEx
rs6704234	RP11-15I11.3	cis	lung	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212526800-212582800	Weak transcription	Fetal Brain Male	brain
2	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
3	chr1:212540400-212575400	Weak transcription	HUVEC	blood vessel
4	chr1:212553200-212578400	Weak transcription	K562	blood
5	chr1:212556800-212587600	Weak transcription	Small Intestine	intestine
6	chr1:212558600-212578800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:212558600-212580000	Weak transcription	Left Ventricle	heart
8	chr1:212560200-212578400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:212560400-212580200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:212560600-212578200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:212560600-212578800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:212560600-212580200	Weak transcription	HSMMtube	muscle
13	chr1:212560600-212582000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:212560600-212582000	Weak transcription	Gastric	stomach
15	chr1:212561000-212575400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:212561000-212578000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:212561000-212579800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:212561000-212579800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:212561000-212580000	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:212561000-212582400	Weak transcription	Aorta	Aorta
21	chr1:212562000-212578400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:212564200-212578800	Weak transcription	Esophagus	oesophagus
23	chr1:212564400-212575400	Weak transcription	Thymus	Thymus
24	chr1:212564600-212576200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:212564600-212577800	Weak transcription	Spleen	Spleen
26	chr1:212564600-212578600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:212564600-212579800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:212569600-212582600	Weak transcription	Ovary	ovary
29	chr1:212570400-212578800	Weak transcription	Fetal Stomach	stomach
30	chr1:212570600-212574400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:212570600-212577200	Strong transcription	Fetal Thymus	thymus
32	chr1:212570600-212577800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:212570600-212578400	Weak transcription	HepG2	liver
34	chr1:212570600-212582000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:212570800-212575400	Weak transcription	HSMM	muscle
36	chr1:212570800-212576000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:212570800-212580000	Weak transcription	Fetal Lung	lung
38	chr1:212571000-212575200	Weak transcription	NHLF	lung
39	chr1:212571000-212578600	Weak transcription	Brain Anterior Caudate	brain
40	chr1:212571000-212586200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:212571200-212574200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:212571200-212575400	Weak transcription	Osteobl	bone
43	chr1:212571200-212576600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:212571200-212578400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:212571200-212580000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:212571400-212574600	Weak transcription	NHEK	skin
47	chr1:212571400-212576200	Weak transcription	Brain Substantia Nigra	brain
48	chr1:212571400-212577800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr1:212571400-212580000	Weak transcription	NH-A	brain
50	chr1:212571600-212574000	Strong transcription	Monocytes-CD14+_RO01746	blood

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