Variant report

Variant	rs11264371
Chromosome Location	chr1:155412037-155412038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155403382..155405033-chr1:155410583..155412465,2	MCF-7	breast:
2	chr1:155406981..155408656-chr1:155410586..155413532,3	K562	blood:
3	chr1:155411983..155412619-chr16:81069239..81069761,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166454	Chromatin interaction
ENSG00000260213	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10752611	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10796943	1.00[CHB][hapmap];0.97[GIH][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10796944	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10796945	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10796946	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10796947	0.91[ASN][1000 genomes]
rs10908463	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap]
rs10908465	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908466	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908467	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10908469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10908470	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10908471	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10908472	0.87[ASN][1000 genomes]
rs11264359	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap]
rs11264361	1.00[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap]
rs11264363	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs11264366	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11264367	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264369	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11264370	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11264372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264374	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264375	0.93[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11264380	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]
rs11264381	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11264383	0.88[ASN][1000 genomes]
rs11264386	0.81[ASN][1000 genomes]
rs11264387	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap]
rs11582072	0.91[ASN][1000 genomes]
rs12025532	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12026638	0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028416	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12030596	0.88[ASN][1000 genomes]
rs12037824	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12041534	0.93[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046473	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12067371	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12079134	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12081067	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12143948	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs12239100	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12239114	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs12724079	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12746592	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1325908	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1360554	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1556488	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap]
rs1886905	0.81[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap]
rs2025669	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2297480	0.89[CHB][hapmap];0.85[MEX][hapmap]
rs35615695	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3892792	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs5005770	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs56675301	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6670014	0.82[AMR][1000 genomes]
rs6677385	0.84[AFR][1000 genomes]
rs6684889	0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs6688636	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6692183	0.84[AFR][1000 genomes]
rs6696888	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7411786	0.87[ASN][1000 genomes]
rs7416976	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7556102	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	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
6	esv1795478	chr1:155334933-155510824	Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	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
8	esv1800974	chr1:155367680-155510824	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11264371	LCE1C	cis	parietal	SCAN
rs11264371	YY1AP1	cis	cerebellum	SCAN
rs11264371	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs11264371	SPRR2D	cis	parietal	SCAN
rs11264371	YY1AP1	cis	parietal	SCAN
rs11264371	GBAP1	cis	parietal	SCAN
rs11264371	GBA	cis	Esophagus Mucosa	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155362200-155433400	Weak transcription	Psoas Muscle	Psoas
2	chr1:155362800-155442400	Weak transcription	Right Ventricle	heart
3	chr1:155364400-155450800	Weak transcription	HUVEC	blood vessel
4	chr1:155367400-155426000	Weak transcription	Stomach Mucosa	stomach
5	chr1:155384800-155425600	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:155392800-155422800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:155399400-155418200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:155402400-155426800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:155404600-155441400	Weak transcription	Esophagus	oesophagus
10	chr1:155405400-155417400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:155407600-155417600	Weak transcription	Fetal Heart	heart
12	chr1:155407600-155425800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:155408400-155428000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:155408600-155444200	Weak transcription	Fetal Brain Male	brain
15	chr1:155408600-155448400	Weak transcription	Fetal Brain Female	brain
16	chr1:155408800-155412600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:155408800-155416200	Weak transcription	HSMM	muscle
18	chr1:155408800-155417400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:155408800-155417400	Weak transcription	Fetal Kidney	kidney
20	chr1:155408800-155417800	Weak transcription	Fetal Lung	lung
21	chr1:155408800-155418000	Weak transcription	Fetal Stomach	stomach
22	chr1:155408800-155418200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:155408800-155419200	Weak transcription	A549	lung
24	chr1:155408800-155419600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:155408800-155419600	Weak transcription	Adipose Nuclei	Adipose
26	chr1:155408800-155419800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:155408800-155419800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:155408800-155419800	Weak transcription	NH-A	brain
29	chr1:155408800-155420000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr1:155408800-155420000	Weak transcription	Fetal Intestine Large	intestine
31	chr1:155408800-155420200	Weak transcription	Colonic Mucosa	Colon
32	chr1:155408800-155420400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:155408800-155420400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:155408800-155420400	Weak transcription	GM12878-XiMat	blood
35	chr1:155408800-155420600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:155408800-155420600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:155408800-155420800	Weak transcription	Brain Germinal Matrix	brain
38	chr1:155408800-155421200	Weak transcription	Lung	lung
39	chr1:155408800-155421200	Weak transcription	Ovary	ovary
40	chr1:155408800-155422400	Weak transcription	Left Ventricle	heart
41	chr1:155408800-155422400	Weak transcription	Pancreas	Pancrea
42	chr1:155408800-155425000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:155408800-155425200	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:155408800-155425200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:155408800-155425200	Weak transcription	Brain Substantia Nigra	brain
46	chr1:155408800-155425200	Weak transcription	HSMMtube	muscle
47	chr1:155408800-155425200	Weak transcription	NHDF-Ad	bronchial
48	chr1:155408800-155425400	Weak transcription	Brain Angular Gyrus	brain
49	chr1:155408800-155425400	Weak transcription	Brain Anterior Caudate	brain
50	chr1:155408800-155425400	Weak transcription	Rectal Smooth Muscle	rectum

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