Variant report

Variant	rs1264695
Chromosome Location	chr6:30067892-30067893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30043035..30044565-chr6:30066202..30069074,2	MCF-7	breast:
2	chr6:30039673..30045870-chr6:30065915..30071954,9	MCF-7	breast:
3	chr6:30059482..30063646-chr6:30064744..30071169,8	MCF-7	breast:
4	chr6:30029240..30031636-chr6:30067690..30069434,2	K562	blood:
5	chr6:30031856..30036259-chr6:30064937..30071315,10	MCF-7	breast:
6	chr6:30027986..30030809-chr6:30067690..30071011,4	K562	blood:
7	chr6:30059663..30061808-chr6:30067229..30070058,2	K562	blood:
8	chr6:30067195..30070112-chr6:30098151..30100617,2	MCF-7	breast:
9	chr6:30027914..30030220-chr6:30065122..30067982,3	MCF-7	breast:
10	chr6:30039276..30042217-chr6:30067253..30069841,2	K562	blood:
11	chr6:30063791..30066840-chr6:30067476..30070156,3	MCF-7	breast:
12	chr6:30067592..30070049-chr6:30312859..30314391,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204618	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000204619	Chromatin interaction
ENSG00000066379	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10947051	0.81[ASN][1000 genomes]
rs10947052	0.81[ASN][1000 genomes]
rs1108052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1108053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1110446	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1110448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1156533	0.91[ASN][1000 genomes]
rs11751554	0.86[ASN][1000 genomes]
rs11753939	0.80[ASN][1000 genomes]
rs11755853	0.81[ASN][1000 genomes]
rs11758516	0.81[ASN][1000 genomes]
rs11965379	0.80[ASN][1000 genomes]
rs11965540	0.80[ASN][1000 genomes]
rs11967911	0.98[ASN][1000 genomes]
rs11968367	0.86[ASN][1000 genomes]
rs11968434	0.86[ASN][1000 genomes]
rs1264694	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1264696	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264702	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12661731	0.91[ASN][1000 genomes]
rs12663534	0.81[ASN][1000 genomes]
rs17187791	0.98[ASN][1000 genomes]
rs17187805	0.98[ASN][1000 genomes]
rs17194146	0.89[ASN][1000 genomes]
rs17194153	0.98[ASN][1000 genomes]
rs17194160	0.98[ASN][1000 genomes]
rs17194174	0.98[ASN][1000 genomes]
rs2072110	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240071	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2248289	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2285805	0.80[ASN][1000 genomes]
rs2394735	0.81[ASN][1000 genomes]
rs2523994	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2524005	1.00[CEU][hapmap]
rs2844796	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28454792	0.96[ASN][1000 genomes]
rs28771211	0.82[ASN][1000 genomes]
rs28780078	0.91[ASN][1000 genomes]
rs28780079	0.91[ASN][1000 genomes]
rs28780080	0.91[ASN][1000 genomes]
rs28780081	0.91[ASN][1000 genomes]
rs28780082	0.90[ASN][1000 genomes]
rs3188482	0.80[ASN][1000 genomes]
rs3807032	0.81[ASN][1000 genomes]
rs3807033	0.81[ASN][1000 genomes]
rs57195817	0.84[ASN][1000 genomes]
rs57518619	0.81[ASN][1000 genomes]
rs58099508	0.81[ASN][1000 genomes]
rs60418878	0.85[ASN][1000 genomes]
rs61666432	0.86[ASN][1000 genomes]
rs6457149	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73424274	0.85[ASN][1000 genomes]
rs73728107	0.80[ASN][1000 genomes]
rs7741418	0.91[ASN][1000 genomes]
rs7749793	0.98[ASN][1000 genomes]
rs7753935	0.98[ASN][1000 genomes]
rs7754005	0.98[ASN][1000 genomes]
rs7761563	0.91[ASN][1000 genomes]
rs7765810	0.91[ASN][1000 genomes]
rs7771071	0.86[ASN][1000 genomes]
rs916569	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916570	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261384	0.91[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	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv884051	chr6:30059451-30071279	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv884050	chr6:30059451-30071330	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv884053	chr6:30059592-30070538	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
5	nsv884054	chr6:30061361-30069525	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
6	nsv524794	chr6:30066031-30067892	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs1264695	ZSCAN23	cis	parietal	SCAN
rs1264695	BTN3A2	cis	parietal	SCAN
rs1264695	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs1264695	HIST1H4G	cis	cerebellum	SCAN
rs1264695	LOC347981	cis	multi-tissue	Pritchard
rs1264695	ZNF323	cis	parietal	SCAN
rs1264695	Hs.519979	cis	multi-tissue	Pritchard
rs1264695	HIST1H2BM	cis	cerebellum	SCAN
rs1264695	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1264695	HIST1H2AM	cis	parietal	SCAN
rs1264695	ABT1	cis	parietal	SCAN
rs1264695	HIST1H2BN	cis	parietal	SCAN
rs1264695	ZNRD1	cis	lymphoblastoid	seeQTL
rs1264695	ZKSCAN3	cis	parietal	SCAN
rs1264695	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30063400-30068400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:30063600-30068200	Weak transcription	HMEC	breast
3	chr6:30063800-30068000	Weak transcription	Lung	lung
4	chr6:30064000-30068000	Enhancers	HepG2	liver
5	chr6:30064800-30068400	Bivalent Enhancer	Fetal Intestine Large	intestine
6	chr6:30064800-30069600	Bivalent Enhancer	Fetal Thymus	thymus
7	chr6:30065400-30068800	Weak transcription	Gastric	stomach
8	chr6:30066200-30068000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:30066200-30068200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:30067000-30068200	Bivalent Enhancer	Fetal Intestine Small	intestine
11	chr6:30067000-30068400	Bivalent Enhancer	Primary T cells from cord blood	blood
12	chr6:30067200-30068000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
13	chr6:30067600-30068000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
14	chr6:30067600-30068000	Bivalent Enhancer	Rectal Smooth Muscle	rectum
15	chr6:30067600-30068200	Enhancers	Duodenum Mucosa	Duodenum
16	chr6:30067600-30068400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
17	chr6:30067600-30068400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
18	chr6:30067800-30068000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
19	chr6:30067800-30068000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
20	chr6:30067800-30068000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
21	chr6:30067800-30068000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:30067800-30068000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr6:30067800-30068200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
24	chr6:30067800-30068200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:30067800-30068200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:30067800-30068200	Weak transcription	Pancreas	Pancrea
27	chr6:30067800-30068200	Bivalent Enhancer	Stomach Mucosa	stomach
28	chr6:30067800-30068400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
29	chr6:30067800-30068400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
30	chr6:30067800-30068400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:30067800-30068400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr6:30067800-30069000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon

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