Variant report

Variant	rs3025000
Chromosome Location	chr6:43746169-43746170
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	chr6:43745073..43748024-chr6:44039738..44042379,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RSPH9-4	chr6:43745457-43746273	NONHSAT112919
2	lnc-RSPH9-4	chr6:43745909-43746273	NONHSAT112920

Variant related genes	Relation type
ENSG00000231881	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13202855	1.00[YRI][hapmap]
rs2010963	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3024997	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3024998	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs699946	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs735286	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs833060	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs833068	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs833069	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs865577	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869383	chr6:43505094-43752189	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
3	nsv1018626	chr6:43694649-43803732	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv885848	chr6:43732669-43753051	Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:43740200-43748000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:43740200-43752200	Weak transcription	Aorta	Aorta
3	chr6:43740800-43755600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:43742600-43746200	Enhancers	Fetal Heart	heart
5	chr6:43742600-43756400	Weak transcription	Primary T cells from cord blood	blood
6	chr6:43742800-43750200	Genic enhancers	Gastric	stomach
7	chr6:43743000-43747200	Genic enhancers	Liver	Liver
8	chr6:43743000-43751000	Genic enhancers	Left Ventricle	heart
9	chr6:43743000-43766400	Weak transcription	HUVEC	blood vessel
10	chr6:43743200-43748800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr6:43743200-43753600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:43743200-43754600	Strong transcription	Dnd41	blood
13	chr6:43743400-43746200	Weak transcription	Fetal Brain Male	brain
14	chr6:43743400-43753800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:43743400-43754600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr6:43743400-43754800	Strong transcription	HSMM	muscle
17	chr6:43743600-43746400	Strong transcription	Fetal Lung	lung
18	chr6:43743600-43747800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr6:43743600-43753400	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr6:43743600-43753600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:43743600-43753600	Strong transcription	NHEK	skin
22	chr6:43743600-43754000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:43743800-43751200	Genic enhancers	Pancreas	Pancrea
24	chr6:43743800-43753600	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr6:43743800-43753800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:43744000-43752200	Genic enhancers	Right Ventricle	heart
27	chr6:43744000-43753600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:43744000-43753800	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:43744000-43753800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr6:43744000-43754400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:43744000-43754600	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr6:43744000-43754600	Strong transcription	Osteobl	bone
33	chr6:43744000-43755000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:43744200-43746800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:43744200-43753600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:43744200-43753600	Strong transcription	Colonic Mucosa	Colon
37	chr6:43744200-43753600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr6:43744200-43754800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:43744200-43755000	Strong transcription	Fetal Intestine Large	intestine
40	chr6:43744200-43757800	Weak transcription	Primary B cells from cord blood	blood
41	chr6:43744400-43746600	Strong transcription	Esophagus	oesophagus
42	chr6:43744400-43747200	Strong transcription	Fetal Stomach	stomach
43	chr6:43744400-43747600	Strong transcription	Hela-S3	cervix
44	chr6:43744400-43748800	Strong transcription	NHLF	lung
45	chr6:43744400-43750600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:43744400-43750800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:43744400-43753400	Strong transcription	A549	lung
48	chr6:43744400-43753800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr6:43744400-43754400	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr6:43744400-43754600	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links