Variant report

Variant	rs1977172
Chromosome Location	chr6:36641754-36641755
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:36640651..36642338-chr6:36646391..36648359,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CPNE5-3	chr6:36641398-36642903	NR_109836

Variant related genes	Relation type
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1321312	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1969701	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3176330	0.91[ASN][1000 genomes]
rs3176331	0.85[ASN][1000 genomes]
rs3829966	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3829967	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3829968	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4135234	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4135237	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4135239	0.93[ASN][1000 genomes]
rs4713997	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4714000	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6457936	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6902994	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6907801	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6926780	1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7452626	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs762623	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9380585	1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9380586	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv13626	chr6:36640176-36642182	Enhancers Weak transcription	CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36631000-36644000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:36635200-36643800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:36635400-36644000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:36635400-36645600	Weak transcription	Small Intestine	intestine
5	chr6:36635600-36644000	Weak transcription	Hela-S3	cervix
6	chr6:36636400-36643800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:36636400-36643800	Weak transcription	NH-A	brain
8	chr6:36637000-36643800	Weak transcription	Osteobl	bone
9	chr6:36637200-36643600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:36637200-36643800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:36637200-36643800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:36637200-36643800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:36637200-36643800	Weak transcription	HSMM	muscle
14	chr6:36637400-36642600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:36637800-36642600	Weak transcription	HSMMtube	muscle
16	chr6:36637800-36643400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:36637800-36643400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:36637800-36643800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:36637800-36643800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:36638800-36644200	Weak transcription	Ovary	ovary
21	chr6:36640000-36643800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:36640000-36643800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:36640000-36644000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:36640200-36642000	Weak transcription	HepG2	liver
25	chr6:36640200-36642400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:36640200-36643800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:36640400-36645600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr6:36640600-36643200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:36640800-36643800	Weak transcription	Fetal Intestine Small	intestine
30	chr6:36641000-36643800	Weak transcription	Fetal Intestine Large	intestine
31	chr6:36641200-36642400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:36641600-36643000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr6:36641600-36643800	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links