Variant report

Variant	rs11264380
Chromosome Location	chr1:155520144-155520145
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155294749..155296662-chr1:155518783..155520938,2	K562	blood:
2	chr1:155515123..155516751-chr1:155518229..155520360,2	K562	blood:
3	chr1:155518733..155520957-chr1:155531970..155533886,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160753	Chromatin interaction
ENSG00000116539	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10752611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10796943	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10796945	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10796946	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10796947	0.95[ASN][1000 genomes]
rs10908465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10908466	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908467	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908469	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10908470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908472	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908479	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs10908481	0.84[CEU][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap]
rs11264367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264369	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264370	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11264371	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11264372	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11264374	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11264375	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264383	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264386	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264393	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11264397	0.85[EUR][1000 genomes]
rs11264398	0.86[EUR][1000 genomes]
rs11582072	0.95[ASN][1000 genomes]
rs12022088	0.85[EUR][1000 genomes]
rs12025532	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12026638	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12028416	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12030596	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035524	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs12037824	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12039893	0.85[EUR][1000 genomes]
rs12040100	0.86[EUR][1000 genomes]
rs12041534	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12046473	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12047626	0.81[EUR][1000 genomes]
rs12047756	0.81[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs12067371	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12079134	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12091730	0.84[AMR][1000 genomes]
rs12093350	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12143948	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs12239100	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12239114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs12724079	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs12740629	0.83[EUR][1000 genomes]
rs12744132	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs12746592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758945	0.82[EUR][1000 genomes]
rs1325908	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1360554	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs1556488	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs1886905	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs2025669	0.82[EUR][1000 genomes]
rs2048431	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs2175391	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs2666826	0.90[JPT][hapmap]
rs34124416	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34620961	0.84[EUR][1000 genomes]
rs348186	0.83[EUR][1000 genomes]
rs348196	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs35615695	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs3738590	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs3851912	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3892792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs475550	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs4971095	0.86[EUR][1000 genomes]
rs5005770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs56675301	0.83[EUR][1000 genomes]
rs6427278	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs644853	1.00[JPT][hapmap]
rs6672128	0.84[EUR][1000 genomes]
rs6684889	0.89[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs6688636	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs6696888	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.99[ASN][1000 genomes]
rs670876	0.80[CEU][hapmap]
rs678157	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs7411786	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7521594	0.84[EUR][1000 genomes]
rs7556102	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs821551	0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]

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	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
2	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
3	esv1799856	chr1:155305059-155534616	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1795662	chr1:155305059-155540660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv1803551	chr1:155334933-155522572	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv872468	chr1:155413304-155549562	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	esv3431739	chr1:155514331-155664183	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11264380	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs11264380	GBAP1	cis	Artery Tibial	GTEx
rs11264380	FDPS	cis	parietal	SCAN
rs11264380	RIT1	cis	cerebellum	SCAN
rs11264380	GBA	cis	Esophagus Mucosa	GTEx
rs11264380	YY1AP1	cis	parietal	SCAN
rs11264380	SPRR2A	cis	cerebellum	SCAN
rs11264380	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs11264380	SPRR2D	cis	parietal	SCAN
rs11264380	YY1AP1	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155483200-155524400	Weak transcription	Fetal Brain Female	brain
2	chr1:155483400-155528600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:155489800-155529400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:155491200-155521800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:155491400-155523400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:155496600-155529800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:155500000-155524400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr1:155501800-155523200	Weak transcription	Brain Hippocampus Middle	brain
9	chr1:155503800-155523200	Weak transcription	Fetal Thymus	thymus
10	chr1:155505600-155523400	Weak transcription	Placenta	Placenta
11	chr1:155506400-155523400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:155506400-155529400	Weak transcription	Osteobl	bone
13	chr1:155506400-155529600	Weak transcription	Fetal Lung	lung
14	chr1:155507000-155530200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:155507400-155528000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:155510600-155530200	Weak transcription	Right Ventricle	heart
17	chr1:155510800-155523600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:155510800-155524400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:155510800-155528000	Weak transcription	Small Intestine	intestine
20	chr1:155510800-155528400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:155511000-155529200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:155511000-155529400	Weak transcription	HepG2	liver
23	chr1:155511400-155529800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:155511800-155527600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:155511800-155528400	Weak transcription	Primary T cells from cord blood	blood
26	chr1:155513200-155524400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:155513600-155520600	Weak transcription	Fetal Muscle Leg	muscle
28	chr1:155513800-155523200	Weak transcription	Thymus	Thymus
29	chr1:155513800-155524400	Weak transcription	A549	lung
30	chr1:155514000-155529400	Weak transcription	Hela-S3	cervix
31	chr1:155514400-155520400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr1:155514400-155520400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:155514400-155521600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:155514400-155521800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr1:155514400-155523600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:155514400-155524800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr1:155514400-155527800	Weak transcription	Liver	Liver
38	chr1:155514400-155528000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:155514400-155528400	Weak transcription	Left Ventricle	heart
40	chr1:155514400-155530200	Weak transcription	Pancreas	Pancrea
41	chr1:155514400-155530200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:155514400-155530200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:155514600-155524400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr1:155514800-155521800	Weak transcription	Fetal Intestine Large	intestine
45	chr1:155515800-155521400	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr1:155516000-155530200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:155516400-155520600	Weak transcription	Fetal Intestine Small	intestine
48	chr1:155516800-155524600	Weak transcription	Primary B cells from cord blood	blood
49	chr1:155516800-155529600	Weak transcription	NHDF-Ad	bronchial
50	chr1:155517000-155521000	Enhancers	Primary B cells from peripheral blood	blood

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