Variant report

Variant	rs9295655
Chromosome Location	chr6:25328153-25328154
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	chr6:25318943..25320704-chr6:25326151..25329125,2	K562	blood:
2	chr6:25326407..25328243-chr6:25331824..25333958,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs16890366	0.81[AFR][1000 genomes]
rs2143023	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2690107	0.88[MEX][hapmap];0.87[TSI][hapmap]
rs2690111	0.83[CHB][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs4712904	0.83[LWK][hapmap]
rs4712905	0.84[LWK][hapmap]
rs55967593	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6906812	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6908260	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6913606	0.81[AFR][1000 genomes]
rs6913886	0.81[AFR][1000 genomes]
rs6915270	0.80[AFR][1000 genomes]
rs6927238	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6932783	0.83[ASN][1000 genomes]
rs7741580	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7743750	0.80[AFR][1000 genomes]
rs7746942	0.94[LWK][hapmap]
rs7755701	0.81[AFR][1000 genomes]
rs7756143	0.81[AFR][1000 genomes]
rs7759796	0.93[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7759828	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7759879	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7760067	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7760151	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7764111	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9295654	0.94[LWK][hapmap];0.81[AFR][1000 genomes]
rs9348671	0.80[AFR][1000 genomes]
rs9348672	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9366615	0.84[JPT][hapmap]
rs9366617	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366618	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9393639	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9393640	0.94[ASN][1000 genomes]
rs9467466	0.94[LWK][hapmap]
rs999039	0.94[LWK][hapmap];0.81[TSI][hapmap];0.83[AFR][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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9295655	LRRC16A	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25306600-25331400	Weak transcription	Spleen	Spleen
2	chr6:25313400-25329800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:25313800-25331400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:25315400-25329600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:25321000-25329400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:25321000-25329600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:25321000-25331400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:25321200-25329200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:25321200-25329400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:25321200-25329400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:25321600-25329200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:25321600-25329400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:25321600-25329600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:25321600-25329800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:25321600-25341200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr6:25323000-25333200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:25324600-25329200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:25324600-25329600	Weak transcription	Brain Substantia Nigra	brain
19	chr6:25324600-25330400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:25324600-25331600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:25325000-25329400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:25325000-25331600	Weak transcription	Adipose Nuclei	Adipose
23	chr6:25325200-25328800	Enhancers	Fetal Heart	heart
24	chr6:25325200-25329400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:25325200-25330200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:25325200-25330200	Weak transcription	Esophagus	oesophagus
27	chr6:25325200-25331400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:25325200-25331400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:25325200-25331400	Weak transcription	Placenta	Placenta
30	chr6:25325200-25331400	Weak transcription	Pancreas	Pancrea
31	chr6:25325200-25331400	Weak transcription	HSMMtube	muscle
32	chr6:25325200-25336400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:25325200-25336400	Weak transcription	Lung	lung
34	chr6:25326600-25328600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:25326600-25329200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr6:25326800-25333000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr6:25327000-25328600	Enhancers	Duodenum Mucosa	Duodenum
38	chr6:25327000-25329200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:25327000-25332600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr6:25327200-25328600	Enhancers	Fetal Brain Female	brain
41	chr6:25327200-25328600	Enhancers	Fetal Lung	lung
42	chr6:25327200-25328600	Enhancers	Stomach Mucosa	stomach
43	chr6:25327200-25328800	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr6:25327200-25329600	Weak transcription	Gastric	stomach
45	chr6:25327400-25328200	Enhancers	HepG2	liver
46	chr6:25327400-25330200	Weak transcription	Right Atrium	heart
47	chr6:25327600-25328200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr6:25327600-25328200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr6:25327600-25328400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:25327600-25329200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links