Variant report

Variant	rs9285516
Chromosome Location	chr6:149398516-149398517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149376456..149387248-chr6:149393069..149406749,44	MCF-7	breast:
2	chr6:149398184..149404330-chr6:149748783..149757211,17	MCF-7	breast:
3	chr6:149397256..149399835-chr6:149636593..149638648,2	MCF-7	breast:
4	chr6:149350906..149355297-chr6:149396132..149403444,27	MCF-7	breast:
5	chr6:149396450..149400811-chr6:149637735..149640677,5	MCF-7	breast:
6	chr6:149397242..149400123-chr6:149865914..149868983,3	MCF-7	breast:
7	chr6:149353899..149354712-chr6:149398410..149398949,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131013	Chromatin interaction
ENSG00000236591	Chromatin interaction
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10457074	0.87[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[ASN][1000 genomes]
rs10872629	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10872630	0.81[JPT][hapmap]
rs10872631	0.87[JPT][hapmap]
rs11755147	0.87[JPT][hapmap]
rs11759315	0.86[JPT][hapmap]
rs12201653	0.87[JPT][hapmap]
rs12211152	0.93[JPT][hapmap]
rs1316535	0.83[ASN][1000 genomes]
rs1317171	0.86[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1320575	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17669693	0.87[JPT][hapmap]
rs17732007	0.87[JPT][hapmap]
rs1934217	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1934220	0.87[JPT][hapmap]
rs2275423	0.82[CEU][hapmap]
rs2340752	0.82[CEU][hapmap]
rs2340798	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2340801	0.82[CEU][hapmap]
rs2340802	0.86[GIH][hapmap];0.96[MEX][hapmap]
rs2486409	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs4243484	0.83[ASN][1000 genomes]
rs4318907	0.82[CEU][hapmap];0.96[MEX][hapmap]
rs4897074	0.87[CEU][hapmap]
rs4897078	0.87[JPT][hapmap]
rs6570920	0.82[CEU][hapmap]
rs6570933	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6570934	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6570935	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6901019	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6901863	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6903827	0.87[JPT][hapmap]
rs6915298	0.86[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6931675	0.87[ASW][hapmap];0.95[CEU][hapmap];0.81[CHD][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6931744	0.91[GIH][hapmap];0.92[MEX][hapmap]
rs6932386	0.87[JPT][hapmap]
rs6935330	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6936176	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6939103	0.87[JPT][hapmap]
rs7738162	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7747463	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7748978	0.88[MEX][hapmap]
rs7756263	0.81[JPT][hapmap]
rs7760242	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7761119	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7765778	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7772696	0.87[JPT][hapmap]
rs7774887	0.82[CEU][hapmap]
rs7776117	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9322166	0.89[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9377187	0.82[CEU][hapmap]
rs9377188	0.92[MEX][hapmap]

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	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9285516	C6orf97	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149354400-149400600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:149362800-149401400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:149369000-149398800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:149382200-149400000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:149382800-149401400	Weak transcription	Esophagus	oesophagus
6	chr6:149385200-149404000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:149387400-149399800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:149387400-149401400	Weak transcription	Lung	lung
9	chr6:149387400-149404200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:149387600-149401800	Weak transcription	Brain Substantia Nigra	brain
11	chr6:149387800-149401000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:149387800-149401000	Weak transcription	Brain Anterior Caudate	brain
13	chr6:149387800-149401000	Weak transcription	Fetal Lung	lung
14	chr6:149388200-149400400	Weak transcription	Placenta	Placenta
15	chr6:149391600-149400800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:149394600-149399000	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:149394600-149399200	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr6:149394800-149398800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:149395000-149399000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:149395000-149399000	Enhancers	HepG2	liver
21	chr6:149395000-149415000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:149395400-149399000	Strong transcription	Primary B cells from cord blood	blood
23	chr6:149395600-149398800	Enhancers	Dnd41	blood
24	chr6:149395600-149401200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:149395800-149398800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:149395800-149401000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr6:149396200-149400600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:149396400-149398600	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr6:149396400-149398800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:149396400-149399000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:149396400-149399000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr6:149396400-149401200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr6:149396600-149399800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr6:149396800-149398800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:149396800-149399200	Enhancers	Osteobl	bone
36	chr6:149396800-149400200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:149396800-149400600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr6:149396800-149403400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr6:149397000-149398600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:149397000-149399000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:149397000-149399000	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr6:149397000-149399000	Enhancers	A549	lung
43	chr6:149397000-149399000	Enhancers	NH-A	brain
44	chr6:149397000-149400400	Weak transcription	Fetal Muscle Leg	muscle
45	chr6:149397200-149398600	Weak transcription	Stomach Mucosa	stomach
46	chr6:149397200-149401400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr6:149397400-149399600	Weak transcription	Ovary	ovary
48	chr6:149397400-149400200	Weak transcription	Fetal Intestine Small	intestine
49	chr6:149397400-149400400	Weak transcription	Fetal Stomach	stomach
50	chr6:149397400-149400400	Weak transcription	Stomach Smooth Muscle	stomach

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