Variant report

Variant	rs1049353
Chromosome Location	chr6:88853635-88853636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10485171	0.82[ASN][1000 genomes]
rs4707436	0.95[CEU][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59299454	0.92[EUR][1000 genomes]
rs7766029	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv604120	chr6:88818965-89198994	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1015298	chr6:88830630-89075508	Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv538355	chr6:88830630-89075508	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1020107	chr6:88838931-88866748	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2763586	chr6:88838943-88867488	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv519365	chr6:88842154-88861698	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv463944	chr6:88842154-88861698	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv463945	chr6:88842154-88861698	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv604121	chr6:88842154-88861698	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1023549	chr6:88842545-88869048	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1049353	SYNCRIP	cis	parietal	SCAN
rs1049353	RNGTT	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88847600-88855800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:88848400-88855000	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:88850000-88855600	Enhancers	Primary B cells from peripheral blood	blood
4	chr6:88850600-88859200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:88852400-88854200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr6:88852400-88873200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:88852600-88854400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr6:88853000-88853800	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
9	chr6:88853200-88854000	Enhancers	HepG2	liver
10	chr6:88853200-88855600	Enhancers	GM12878-XiMat	blood
11	chr6:88853400-88853800	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr6:88853400-88854000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:88853400-88855400	Weak transcription	Brain Angular Gyrus	brain
14	chr6:88853400-88855800	Strong transcription	Stomach Smooth Muscle	stomach
15	chr6:88853600-88853800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:88853600-88853800	Genic enhancers	Brain Germinal Matrix	brain
17	chr6:88853600-88853800	Flanking Active TSS	Brain Hippocampus Middle	brain
18	chr6:88853600-88853800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:88853600-88853800	Enhancers	Brain Substantia Nigra	brain
20	chr6:88853600-88854000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:88853600-88854000	Active TSS	Brain Cingulate Gyrus	brain
22	chr6:88853600-88854000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr6:88853600-88854400	ZNF genes & repeats	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links