Variant report

Variant	rs12564487
Chromosome Location	chr1:180868417-180868418
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180866617..180870349-chr1:180876247..180878371,3	MCF-7	breast:
2	chr1:180868023..180870697-chr1:180871039..180876030,6	K562	blood:
3	chr1:180863020..180866201-chr1:180866515..180869291,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-XPR1-1	chr1:180868088-180869874	XLOC_000478

Variant related genes	Relation type
ENSG00000225857	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1043069	0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs10494532	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs1061015	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1061016	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs10737351	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs10753223	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10798788	0.92[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10798789	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10798792	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10798793	0.93[CEU][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10798794	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10798795	0.91[ASN][1000 genomes]
rs10914074	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs10914076	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs10914077	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs10914080	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs10914083	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs10914084	0.80[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap]
rs10914095	0.86[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10914107	0.86[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10914111	0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10914112	0.91[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10914113	0.81[ASN][1000 genomes]
rs10914117	0.84[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10914123	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10914124	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs11585146	0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12022782	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs12064862	0.81[ASN][1000 genomes]
rs12064913	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12118635	0.82[CHB][hapmap]
rs12119247	0.83[ASN][1000 genomes]
rs12120511	0.86[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12120522	0.83[ASN][1000 genomes]
rs12120797	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12121436	0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs12131056	0.88[EUR][1000 genomes]
rs12137673	0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12142163	0.84[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12143674	0.91[ASN][1000 genomes]
rs12143915	0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12562489	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs12725006	0.84[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1533422	0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1554183	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs1554184	0.83[ASN][1000 genomes]
rs1554185	0.84[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs17373584	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs1973674	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1980157	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2138399	0.81[ASN][1000 genomes]
rs2176183	0.83[ASN][1000 genomes]
rs2176184	0.81[ASN][1000 genomes]
rs2271669	0.84[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2331887	0.83[ASN][1000 genomes]
rs2944261	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3002118	0.93[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3002119	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34111145	0.83[ASN][1000 genomes]
rs3761903	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3789367	0.86[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs3789368	0.83[ASN][1000 genomes]
rs3789369	0.83[ASN][1000 genomes]
rs3789370	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3789373	0.84[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs3856060	0.86[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs3908048	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4259606	0.83[EUR][1000 genomes]
rs4454505	0.82[ASN][1000 genomes]
rs4550006	0.92[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs4598454	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4652525	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs4652526	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4652527	0.86[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs4652528	0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4652529	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4652530	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4652531	0.81[ASN][1000 genomes]
rs4652533	0.83[ASN][1000 genomes]
rs4652535	0.81[ASN][1000 genomes]
rs61811244	0.91[ASN][1000 genomes]
rs6425655	0.84[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs6661417	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs6677349	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6677506	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6677681	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs6689104	0.81[ASN][1000 genomes]
rs6700926	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs6702006	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6703189	0.86[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7349119	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7516646	0.84[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7536258	0.92[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7546227	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs7546516	0.86[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7548261	0.84[JPT][hapmap]
rs7548671	0.84[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs7555356	0.86[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7556592	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9661675	0.91[EUR][1000 genomes]
rs9701903	0.81[ASN][1000 genomes]
rs9919167	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats 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 target site	97 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180805800-180881000	Weak transcription	Aorta	Aorta
2	chr1:180824000-180880800	Weak transcription	Right Ventricle	heart
3	chr1:180835800-180870400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:180844200-180872200	Weak transcription	Esophagus	oesophagus
5	chr1:180845800-180869000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:180847400-180875400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:180852000-180870400	Weak transcription	A549	lung
8	chr1:180857600-180869600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:180858400-180870600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:180861200-180880800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:180864600-180870200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:180867000-180868600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:180867200-180869200	Enhancers	H9 Cell Line	embryonic stem cell
14	chr1:180867400-180868600	Enhancers	NHDF-Ad	bronchial
15	chr1:180867400-180868800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:180867400-180868800	Enhancers	Placenta	Placenta
17	chr1:180867400-180869000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr1:180867400-180869200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:180867400-180869200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:180867400-180869200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:180867400-180869600	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr1:180867600-180868600	Enhancers	Fetal Muscle Leg	muscle
23	chr1:180867600-180868800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:180867600-180868800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:180867600-180869400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:180867600-180869400	Enhancers	Fetal Muscle Trunk	muscle
27	chr1:180867600-180869400	Weak transcription	Pancreas	Pancrea
28	chr1:180867600-180869600	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr1:180867600-180869800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr1:180867600-180869800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:180867800-180868600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:180867800-180869200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:180868000-180868800	Enhancers	Right Atrium	heart
34	chr1:180868000-180869000	Enhancers	Fetal Thymus	thymus
35	chr1:180868000-180870600	Weak transcription	Brain Germinal Matrix	brain
36	chr1:180868000-180878600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:180868400-180868800	Bivalent Enhancer	Fetal Stomach	stomach
38	chr1:180868400-180869000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:180868400-180869600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:180868400-180869800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:180868400-180878400	Weak transcription	Fetal Lung	lung

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