Variant report

Variant	rs6674621
Chromosome Location	chr1:225765235-225765236
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	chr1:225765171..225767134-chr1:225838958..225842433,3	MCF-7	breast:
2	chr1:225749423..225753817-chr1:225762861..225765930,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LBR-3	chr1:225765121-225765292	NONHSAT009842

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10449249	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10915829	0.87[ASN][1000 genomes]
rs11377355	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026034	0.87[ASN][1000 genomes]
rs12031208	0.83[ASN][1000 genomes]
rs12031651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12037289	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038373	1.00[CEU][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12042273	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042698	0.80[ASN][1000 genomes]
rs12239415	0.82[ASN][1000 genomes]
rs1340870	0.83[ASN][1000 genomes]
rs1340871	0.87[ASN][1000 genomes]
rs1340872	0.87[ASN][1000 genomes]
rs16845000	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2184778	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]
rs2185531	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296880	0.89[EUR][1000 genomes]
rs2297747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs28620013	0.87[ASN][1000 genomes]
rs3766931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795443	1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[ASN][1000 genomes]
rs4129816	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55751087	0.81[ASN][1000 genomes]
rs56090476	0.84[AFR][1000 genomes]
rs56169721	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58269599	0.87[ASN][1000 genomes]
rs58696877	0.81[EUR][1000 genomes]
rs59912270	0.87[ASN][1000 genomes]
rs61333083	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6681559	0.87[ASN][1000 genomes]
rs6684314	0.87[ASN][1000 genomes]
rs6684956	0.85[ASN][1000 genomes]
rs6694938	0.84[ASN][1000 genomes]
rs74146931	0.82[ASN][1000 genomes]
rs74146994	0.87[ASN][1000 genomes]
rs74149835	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74149844	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415548	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7543444	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6674621	LBR	cis	Esophagus Muscularis	GTEx
rs6674621	LBR	cis	Artery Tibial	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225730600-225765800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:225730600-225776200	Weak transcription	Pancreas	Pancrea
3	chr1:225744800-225768200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:225744800-225768600	Weak transcription	Fetal Brain Male	brain
5	chr1:225745000-225770000	Weak transcription	HUVEC	blood vessel
6	chr1:225745000-225772800	Weak transcription	Fetal Brain Female	brain
7	chr1:225748800-225765800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:225748800-225799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:225749200-225783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:225754400-225769400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:225754600-225766000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:225755200-225766000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:225755200-225772200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:225756600-225767600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:225756800-225765400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:225758200-225765800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:225759400-225769600	Weak transcription	Lung	lung
18	chr1:225759600-225787600	Weak transcription	Fetal Intestine Small	intestine
19	chr1:225760000-225769800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:225761200-225765800	Weak transcription	Fetal Kidney	kidney
22	chr1:225761800-225765800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:225762000-225768600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:225762800-225766400	Enhancers	Brain Angular Gyrus	brain
25	chr1:225763000-225765400	Enhancers	Brain Hippocampus Middle	brain
26	chr1:225763000-225766600	Enhancers	Rectal Smooth Muscle	rectum
27	chr1:225763200-225766400	Enhancers	Colon Smooth Muscle	Colon
28	chr1:225763400-225766600	Enhancers	A549	lung
29	chr1:225763800-225768200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:225764000-225768000	Weak transcription	Psoas Muscle	Psoas
31	chr1:225764200-225765600	Enhancers	Brain Substantia Nigra	brain
32	chr1:225764200-225765800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:225764200-225766400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:225764200-225766400	Enhancers	Brain Anterior Caudate	brain
35	chr1:225764200-225766600	Enhancers	Fetal Lung	lung
36	chr1:225764200-225766800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:225764200-225767200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr1:225764200-225768600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:225764400-225766200	Enhancers	Fetal Muscle Leg	muscle
40	chr1:225764400-225766200	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:225764400-225766400	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr1:225764400-225766400	Enhancers	Osteobl	bone
43	chr1:225764400-225766800	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr1:225764400-225766800	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr1:225764400-225766800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:225764400-225767000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:225764400-225767200	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr1:225764400-225768600	Enhancers	Fetal Heart	heart
49	chr1:225764600-225766200	Enhancers	Ovary	ovary
50	chr1:225764600-225766800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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