Variant report

Variant	rs2184778
Chromosome Location	chr1:225699681-225699682
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225698646..225701113-chr1:225965307..225966901,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143742	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10449249	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10915829	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11377355	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12022013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12026034	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12031208	0.85[ASN][1000 genomes]
rs12031651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12037289	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12038373	1.00[CEU][hapmap];0.94[CHD][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs12042273	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12042698	0.82[ASN][1000 genomes]
rs12239415	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1340866	0.84[AMR][1000 genomes]
rs1340870	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1340871	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1340872	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16845000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185531	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296880	0.84[EUR][1000 genomes]
rs2297747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs28620013	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3766931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795443	1.00[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs4129816	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487591	0.82[YRI][hapmap]
rs55751087	0.87[AMR][1000 genomes]
rs56169721	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58269599	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59912270	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61333083	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6674621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681559	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6684314	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6684956	0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6694938	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs74146931	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs74146994	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs74149835	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74149844	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7415548	0.92[EUR][1000 genomes]
rs7543444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv2756886	chr1:225665694-225703485	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv2759003	chr1:225665694-225703485	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv4720	chr1:225673218-225718009	Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2184778	LBR	cis	Artery Tibial	GTEx
rs2184778	LBR	cis	Esophagus Muscularis	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225677200-225703600	Weak transcription	Fetal Brain Female	brain
2	chr1:225681800-225699800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:225686800-225699800	Weak transcription	Adipose Nuclei	Adipose
4	chr1:225687000-225705000	Weak transcription	Spleen	Spleen
5	chr1:225687400-225704400	Weak transcription	Fetal Stomach	stomach
6	chr1:225688600-225704600	Weak transcription	Placenta	Placenta
7	chr1:225688800-225711400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:225689200-225721000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:225691000-225706200	Weak transcription	Primary B cells from cord blood	blood
10	chr1:225691200-225705000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:225692600-225704800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:225693200-225702800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:225695400-225704800	Weak transcription	Fetal Brain Male	brain
14	chr1:225695600-225721200	Weak transcription	Fetal Kidney	kidney
15	chr1:225696600-225701800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:225696600-225705000	Weak transcription	Gastric	stomach
17	chr1:225696800-225704800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:225697000-225701200	Strong transcription	Fetal Lung	lung
19	chr1:225697000-225701200	Weak transcription	HepG2	liver
20	chr1:225697200-225699800	Weak transcription	HSMMtube	muscle
21	chr1:225697200-225701400	Weak transcription	Fetal Intestine Small	intestine
22	chr1:225697200-225703400	Weak transcription	Ovary	ovary
23	chr1:225697200-225704800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:225697200-225704800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:225697200-225704800	Weak transcription	Pancreas	Pancrea
26	chr1:225697200-225705000	Weak transcription	Esophagus	oesophagus
27	chr1:225697200-225705000	Weak transcription	Lung	lung
28	chr1:225697200-225705400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:225697200-225711200	Weak transcription	Fetal Heart	heart
30	chr1:225697200-225716600	Weak transcription	Right Atrium	heart
31	chr1:225697400-225700000	Weak transcription	Colon Smooth Muscle	Colon
32	chr1:225697400-225701400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:225697400-225705000	Weak transcription	Aorta	Aorta
34	chr1:225697400-225705000	Weak transcription	Right Ventricle	heart
35	chr1:225697400-225715400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:225697400-225722600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:225697600-225702200	Weak transcription	Stomach Mucosa	stomach
38	chr1:225697600-225703400	Weak transcription	Brain Angular Gyrus	brain
39	chr1:225697600-225703800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:225697800-225699800	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:225697800-225701600	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr1:225697800-225701600	Strong transcription	HSMM	muscle
43	chr1:225697800-225702200	Strong transcription	Osteobl	bone
44	chr1:225697800-225703000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:225697800-225703400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:225697800-225703400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:225697800-225703400	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:225697800-225703800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:225697800-225704800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:225697800-225705400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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