Variant report

Variant	rs6693449
Chromosome Location	chr1:10097672-10097673
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10009323..10011578-chr1:10096303..10099000,2	MCF-7	breast:
2	chr1:10093253..10094828-chr1:10097615..10099498,2	MCF-7	breast:
3	chr1:10091918..10095443-chr1:10096462..10100603,6	K562	blood:
4	chr1:10097355..10099417-chr1:10104304..10106089,2	K562	blood:

Variant related genes	Relation type
ENSG00000130939	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10864442	0.83[AFR][1000 genomes]
rs3003376	0.83[EUR][1000 genomes]
rs3013788	0.83[EUR][1000 genomes]
rs3123522	0.83[EUR][1000 genomes]
rs58528460	0.89[EUR][1000 genomes]
rs61650275	0.82[EUR][1000 genomes]
rs6541075	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6676280	0.84[EUR][1000 genomes]
rs7528979	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7539725	0.80[EUR][1000 genomes]
rs9919194	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][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	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh 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	39 gene(s)	inside rSNPs	diseases
3	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6693449	LZIC	cis	multi-tissue	Pritchard
rs6693449	LZIC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10093800-10097800	Weak transcription	Spleen	Spleen
2	chr1:10094000-10102800	Weak transcription	Pancreas	Pancrea
3	chr1:10094000-10104200	Weak transcription	Gastric	stomach
4	chr1:10094600-10106000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:10094800-10098000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:10094800-10105000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:10094800-10105200	Weak transcription	Right Ventricle	heart
8	chr1:10094800-10105200	Weak transcription	Small Intestine	intestine
9	chr1:10094800-10106000	Weak transcription	Colonic Mucosa	Colon
10	chr1:10094800-10106200	Weak transcription	Stomach Mucosa	stomach
11	chr1:10094800-10119400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:10095000-10097800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:10095000-10098000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:10095000-10098400	Weak transcription	Primary B cells from cord blood	blood
15	chr1:10095000-10098400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:10095000-10098400	Weak transcription	Ovary	ovary
17	chr1:10095000-10098600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr1:10095000-10099200	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:10095000-10099800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:10095000-10100200	Weak transcription	HepG2	liver
21	chr1:10095000-10100800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:10095000-10102200	Weak transcription	Fetal Kidney	kidney
23	chr1:10095000-10102600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:10095000-10104400	Weak transcription	Brain Anterior Caudate	brain
25	chr1:10095000-10104400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:10095000-10104400	Weak transcription	Esophagus	oesophagus
27	chr1:10095000-10104600	Weak transcription	Brain Angular Gyrus	brain
28	chr1:10095000-10104600	Weak transcription	Fetal Heart	heart
29	chr1:10095000-10105200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:10095000-10105200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:10095000-10105200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:10095000-10105200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:10095000-10105200	Weak transcription	Brain Germinal Matrix	brain
34	chr1:10095000-10105200	Weak transcription	Right Atrium	heart
35	chr1:10095000-10105400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:10095000-10105800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:10095000-10106000	Weak transcription	NHDF-Ad	bronchial
38	chr1:10095000-10106200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:10095000-10106200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:10095000-10108000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:10095000-10111400	Weak transcription	GM12878-XiMat	blood
42	chr1:10095000-10115000	Weak transcription	A549	lung
43	chr1:10095000-10115400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:10095000-10116000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:10095000-10116200	Weak transcription	HSMM	muscle
46	chr1:10095000-10127800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr1:10095000-10147600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:10095200-10097800	Weak transcription	NHLF	lung
49	chr1:10095200-10098200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:10095200-10101200	Weak transcription	Fetal Brain Female	brain

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