Variant report

Variant	rs6708858
Chromosome Location	chr2:10098227-10098228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10091577..10093629-chr2:10095328..10098444,3	MCF-7	breast:
2	chr2:10089749..10091694-chr2:10096424..10099200,2	K562	blood:
3	chr2:10097888..10100704-chr2:10102751..10105130,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYS1-6	chr2:10096709-10098242	l_1773_chr2:10096708-10100244_kidney

Variant related genes	Relation type
ENSG00000134317	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2116016	0.81[ASW][hapmap];0.92[LWK][hapmap];0.82[MKK][hapmap]
rs2303918	0.94[ASW][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs3791765	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7581701	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7581717	0.90[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	nsv948591	chr2:9922257-10141191	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv1843231	chr2:9979766-10141191	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6708858	GREB1	cis	parietal	SCAN
rs6708858	GRHL1	cis	multi-tissue	Pritchard

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10092600-10104200	Weak transcription	Lung	lung
2	chr2:10092600-10112600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:10092600-10113400	Weak transcription	Left Ventricle	heart
4	chr2:10092800-10101000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:10092800-10101200	Weak transcription	Brain Angular Gyrus	brain
6	chr2:10092800-10110600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:10093200-10101200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:10093200-10105600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:10093200-10110600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:10093400-10100800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:10093600-10100600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:10093600-10100600	Weak transcription	K562	blood
13	chr2:10093600-10104400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:10093600-10112600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:10094000-10098800	Weak transcription	Adipose Nuclei	Adipose
16	chr2:10094000-10101000	Weak transcription	Dnd41	blood
17	chr2:10094800-10104400	Weak transcription	Fetal Intestine Small	intestine
18	chr2:10094800-10110400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:10094800-10124400	Weak transcription	Fetal Intestine Large	intestine
20	chr2:10095000-10100600	Weak transcription	Brain Germinal Matrix	brain
21	chr2:10095000-10105400	Weak transcription	Pancreas	Pancrea
22	chr2:10095000-10112600	Weak transcription	Hela-S3	cervix
23	chr2:10095200-10104000	Weak transcription	Gastric	stomach
24	chr2:10095400-10100200	Strong transcription	HepG2	liver
25	chr2:10096000-10100600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:10096000-10101200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:10096000-10104000	Weak transcription	Esophagus	oesophagus
28	chr2:10096600-10099000	Weak transcription	Liver	Liver
29	chr2:10098200-10098600	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links