Variant report

Variant	rs11264359
Chromosome Location	chr1:155282829-155282830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155264765..155268361-chr1:155281187..155284828,3	K562	blood:
2	chr1:155246251..155249792-chr1:155281813..155284527,3	K562	blood:
3	chr1:155228693..155233633-chr1:155276892..155283389,6	K562	blood:
4	chr1:155276713..155281137-chr1:155281789..155284748,5	MCF-7	breast:
5	chr1:155232261..155234786-chr1:155281674..155283762,2	K562	blood:

Variant related genes	Relation type
ENSG00000176444	Chromatin interaction
ENSG00000116521	Chromatin interaction
ENSG00000160752	Chromatin interaction
ENSG00000143630	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1052176	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1052177	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10752610	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs1078699	0.91[AFR][1000 genomes]
rs10796941	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10796943	0.94[CHB][hapmap];0.87[TSI][hapmap]
rs10796945	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap]
rs10908461	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10908462	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10908463	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10908465	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap]
rs10908468	0.92[LWK][hapmap];1.00[YRI][hapmap]
rs10908469	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11264349	0.86[EUR][1000 genomes]
rs11264352	0.86[EUR][1000 genomes]
rs11264353	0.86[EUR][1000 genomes]
rs11264354	0.85[EUR][1000 genomes]
rs11264355	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11264357	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11264358	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264361	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11264363	0.89[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap]
rs11264367	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11264369	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11264371	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap]
rs11264372	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11264375	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs12026638	0.90[CHB][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap]
rs12032720	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12041534	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs12042020	0.82[AFR][1000 genomes]
rs12044063	0.85[EUR][1000 genomes]
rs12049375	0.86[EUR][1000 genomes]
rs12067675	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12079134	0.80[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12239114	0.84[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs12724079	0.95[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs12724449	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12749306	0.87[EUR][1000 genomes]
rs1325908	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1360554	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1886905	0.80[CEU][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs2071053	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2242576	0.91[AFR][1000 genomes]
rs2297480	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3020781	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3814318	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3814319	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4472748	0.96[YRI][hapmap]
rs4620533	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4971051	0.96[YRI][hapmap]
rs4971072	0.86[ASN][1000 genomes]
rs4971075	0.81[LWK][hapmap];0.96[YRI][hapmap]
rs5005770	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs6672284	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6684889	0.83[CHB][hapmap]
rs6688636	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7340058	0.92[LWK][hapmap];0.96[YRI][hapmap]
rs7520184	0.86[EUR][1000 genomes]
rs7524950	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7534795	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7543234	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7549276	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7554780	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7556102	0.91[JPT][hapmap]
rs8177968	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8847	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs932972	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
2	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh 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	452 gene(s)	inside rSNPs	diseases
3	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
4	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
5	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
6	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs11264359	PKLR	cis	Nerve Tibial	GTEx
rs11264359	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs11264359	DCST1	cis	parietal	SCAN
rs11264359	THEM5	cis	parietal	SCAN
rs11264359	FDPS	cis	lymphoblastoid	seeQTL
rs11264359	GBAP1	cis	Artery Tibial	GTEx
rs11264359	THBS3	cis	Whole Blood	GTEx
rs11264359	GBAP1	cis	parietal	SCAN
rs11264359	SPRR2A	cis	cerebellum	SCAN
rs11264359	GBA	cis	Esophagus Mucosa	GTEx
rs11264359	LCE1C	cis	parietal	SCAN
rs11264359	SPRR2D	cis	parietal	SCAN
rs11264359	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs11264359	YY1AP1	cis	cerebellum	SCAN
rs11264359	RIT1	cis	cerebellum	SCAN
rs11264359	GBAP1	cis	Thyroid	GTEx
rs11264359	ADAM15	cis	multi-tissue	Pritchard
rs11264359	LAMTOR2	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155278400-155283600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:155279200-155290400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:155279400-155283400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:155279600-155284200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:155279800-155283200	Weak transcription	Aorta	Aorta
6	chr1:155279800-155290400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:155280000-155283000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:155280000-155285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:155280000-155286800	Weak transcription	Brain Anterior Caudate	brain
10	chr1:155280000-155287200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:155280000-155287800	Weak transcription	Brain Angular Gyrus	brain
12	chr1:155280000-155290000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:155280000-155290200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:155280000-155290200	Weak transcription	Right Atrium	heart
15	chr1:155280000-155290400	Weak transcription	Psoas Muscle	Psoas
16	chr1:155280200-155283000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:155280200-155283000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:155280200-155283600	Strong transcription	A549	lung
19	chr1:155280200-155285000	Strong transcription	Fetal Intestine Small	intestine
20	chr1:155280200-155288200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:155280200-155289800	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr1:155280200-155289800	Strong transcription	Fetal Stomach	stomach
23	chr1:155280200-155290000	Weak transcription	Colon Smooth Muscle	Colon
24	chr1:155280200-155290400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:155280200-155290400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:155280400-155283000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:155280400-155283000	Weak transcription	Gastric	stomach
28	chr1:155280400-155283000	Weak transcription	HSMM	muscle
29	chr1:155280400-155285200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:155280400-155285200	Strong transcription	Thymus	Thymus
31	chr1:155280600-155283000	Strong transcription	Fetal Muscle Leg	muscle
32	chr1:155280600-155283000	Weak transcription	Right Ventricle	heart
33	chr1:155280600-155283400	Strong transcription	Fetal Kidney	kidney
34	chr1:155280600-155283600	Strong transcription	Primary T cells from cord blood	blood
35	chr1:155280600-155283600	Strong transcription	Osteobl	bone
36	chr1:155280600-155283800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr1:155280600-155284000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:155280600-155285000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:155280600-155285200	Strong transcription	Esophagus	oesophagus
40	chr1:155280600-155285400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:155280600-155289800	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:155280600-155289800	Weak transcription	Fetal Brain Male	brain
43	chr1:155280600-155290200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:155280600-155290200	Weak transcription	Brain Substantia Nigra	brain
45	chr1:155280800-155283400	Genic enhancers	NHEK	skin
46	chr1:155280800-155284200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:155280800-155285000	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:155280800-155285000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:155280800-155285000	Strong transcription	Stomach Smooth Muscle	stomach
50	chr1:155280800-155290000	Strong transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links