Variant report

Variant	rs554992
Chromosome Location	chr1:225774760-225774761
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225774139..225778253-chr1:225781548..225783833,3	K562	blood:
2	chr1:225766683..225770492-chr1:225772609..225774921,3	MCF-7	breast:
3	chr1:225772554..225774967-chr1:225778509..225781013,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LBR-3	chr1:225774722-225774801	NONHSAT009842

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10753406	0.87[EUR][1000 genomes]
rs10799311	0.81[EUR][1000 genomes]
rs10799314	0.82[ASN][1000 genomes]
rs10799316	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs10799317	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10799318	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10915828	0.93[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs10915830	0.80[EUR][1000 genomes]
rs10915833	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10915834	0.85[EUR][1000 genomes]
rs10915837	0.81[ASN][1000 genomes]
rs10915839	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10915847	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11584675	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12028305	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1222440	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12729655	0.81[ASN][1000 genomes]
rs2639703	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2639716	0.90[EUR][1000 genomes]
rs2657564	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2657569	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs2840958	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2840967	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs2840968	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs3820226	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3856156	0.87[EUR][1000 genomes]
rs4653643	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs476540	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs487591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs498350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510293	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs511649	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516249	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551996	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561656	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426076	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6668770	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6676201	0.81[ASN][1000 genomes]
rs6697783	0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs6702555	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs712062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515907	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7515963	0.81[ASN][1000 genomes]
rs7524766	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7540181	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7541598	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7555139	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7555553	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs812523	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9804142	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs554992	ENAH	cis	normal skin	skin_eQTL
rs554992	LBR	cis	Artery Tibial	GTEx
rs554992	RP11-496N12.9	cis	Thyroid	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225730600-225776200	Weak transcription	Pancreas	Pancrea
2	chr1:225748800-225799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:225749200-225783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:225759600-225787600	Weak transcription	Fetal Intestine Small	intestine
5	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:225766400-225780000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:225766400-225783600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:225766600-225779600	Weak transcription	NH-A	brain
9	chr1:225768400-225781200	Weak transcription	Right Ventricle	heart
10	chr1:225768600-225787800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:225768800-225781000	Weak transcription	HSMM	muscle
12	chr1:225768800-225805600	Weak transcription	Aorta	Aorta
13	chr1:225769000-225783000	Weak transcription	HSMMtube	muscle
14	chr1:225769200-225775000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:225769200-225779800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:225769200-225783200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:225769400-225779600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:225770000-225780000	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:225770000-225782000	Weak transcription	Right Atrium	heart
20	chr1:225770000-225783200	Weak transcription	Psoas Muscle	Psoas
21	chr1:225770000-225785200	Weak transcription	Left Ventricle	heart
22	chr1:225770000-225787600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:225770200-225779600	Weak transcription	Fetal Lung	lung
24	chr1:225770400-225778200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:225770400-225780000	Weak transcription	Ovary	ovary
26	chr1:225770600-225775200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:225770600-225776200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:225770600-225776600	Weak transcription	A549	lung
29	chr1:225770600-225777800	Weak transcription	Fetal Heart	heart
30	chr1:225770600-225778200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:225770600-225779600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:225770600-225779800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:225770800-225775800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:225770800-225776000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:225770800-225781800	Weak transcription	Osteobl	bone
36	chr1:225771000-225779600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:225771000-225784000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:225772600-225775400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:225772800-225775200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:225774000-225780600	Weak transcription	Fetal Stomach	stomach
41	chr1:225774000-225781000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:225774200-225777000	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr1:225774400-225775000	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr1:225774400-225776600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:225774600-225775800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr1:225774600-225776200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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