Variant report

Variant	rs74149835
Chromosome Location	chr1:225718037-225718038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225716258..225718106-chr1:225719282..225721032,2	MCF-7	breast:
2	chr1:225703740..225706678-chr1:225717251..225719258,2	K562	blood:
3	chr1:225712005..225714955-chr1:225715137..225718400,3	K562	blood:
4	chr1:225717290..225720018-chr1:225721925..225724393,2	K562	blood:
5	chr1:225712577..225715165-chr1:225716923..225719442,2	MCF-7	breast:
6	chr1:225710717..225715059-chr1:225715137..225718400,6	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10449249	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915829	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11377355	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022013	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026034	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12031208	0.83[ASN][1000 genomes]
rs12031651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12037289	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038373	0.94[EUR][1000 genomes]
rs12042273	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042698	0.80[ASN][1000 genomes]
rs12239415	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1340870	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1340871	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1340872	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16845000	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2184778	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2185531	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296880	0.86[EUR][1000 genomes]
rs2297747	0.83[ASN][1000 genomes]
rs28620013	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3766931	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795443	0.84[ASN][1000 genomes]
rs4129816	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55751087	0.81[ASN][1000 genomes]
rs56169721	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58269599	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59912270	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61333083	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6674621	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681559	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6684314	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6684956	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6694938	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs74146931	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs74146994	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs74149844	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415548	0.94[EUR][1000 genomes]
rs7543444	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs74149835	LBR	cis	Artery Tibial	GTEx
rs74149835	LBR	cis	Esophagus Muscularis	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225689200-225721000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:225695600-225721200	Weak transcription	Fetal Kidney	kidney
3	chr1:225697400-225722600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:225698600-225721000	Weak transcription	Small Intestine	intestine
5	chr1:225700000-225726400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:225700000-225726400	Weak transcription	HMEC	breast
7	chr1:225701400-225727200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:225701400-225744400	Weak transcription	HUVEC	blood vessel
9	chr1:225701400-225747000	Weak transcription	Hela-S3	cervix
10	chr1:225704200-225721000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:225705600-225747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:225705800-225718800	Weak transcription	Lung	lung
13	chr1:225705800-225726600	Weak transcription	NHEK	skin
14	chr1:225707200-225726600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:225707200-225755000	Weak transcription	Gastric	stomach
16	chr1:225707400-225726600	Weak transcription	Brain Angular Gyrus	brain
17	chr1:225709000-225721000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:225709200-225720000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:225711000-225718800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:225711200-225718800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:225711400-225726600	Weak transcription	Fetal Brain Female	brain
22	chr1:225711600-225720600	Weak transcription	Fetal Intestine Small	intestine
23	chr1:225711600-225720600	Weak transcription	HSMMtube	muscle
24	chr1:225711600-225721200	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:225712400-225719200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:225712400-225729600	Weak transcription	Right Ventricle	heart
27	chr1:225712800-225719000	Strong transcription	Osteobl	bone
28	chr1:225713000-225719000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:225713600-225719400	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr1:225713800-225721000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:225714200-225719200	Strong transcription	A549	lung
32	chr1:225714800-225729600	Weak transcription	Ovary	ovary
33	chr1:225715000-225719000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:225715000-225721000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:225715200-225719400	Weak transcription	Adipose Nuclei	Adipose
36	chr1:225715400-225719200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:225715600-225718200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:225715600-225720600	Weak transcription	Fetal Heart	heart
39	chr1:225715600-225720800	Weak transcription	Fetal Brain Male	brain
40	chr1:225715600-225721000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:225715800-225718400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:225715800-225719000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:225716000-225718600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:225716000-225718800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:225716000-225719200	Strong transcription	HSMM	muscle
46	chr1:225716000-225720000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:225716200-225718400	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:225716200-225718400	Strong transcription	Fetal Lung	lung
49	chr1:225716200-225718600	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:225716200-225718800	Strong transcription	HUES48 Cell Line	embryonic stem cell

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