Variant report

Variant	rs1938925
Chromosome Location	chr11:86344838-86344839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86336049..86341479-chr11:86341893..86346875,7	MCF-7	breast:
2	chr11:86343699..86345284-chr11:86380600..86383529,2	MCF-7	breast:
3	chr11:86343672..86346376-chr11:86522786..86524329,2	MCF-7	breast:
4	chr11:86342318..86349364-chr11:86509780..86514935,13	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRSS23-4	chr11:86344737-86344950	l_530_chr11:86344324-86389623_testes

Variant related genes	Relation type
ENSG00000151376	Chromatin interaction
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10219173	0.96[ASN][1000 genomes]
rs10219305	0.98[ASN][1000 genomes]
rs10219319	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10219378	0.97[ASN][1000 genomes]
rs10400291	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10792860	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10792861	0.92[ASN][1000 genomes]
rs10792862	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10792863	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10792864	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10792866	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10898505	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10898507	0.87[ASN][1000 genomes]
rs10898510	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10898511	0.82[ASN][1000 genomes]
rs10898512	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10898514	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10898515	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10898516	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs11234717	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11535845	0.91[ASN][1000 genomes]
rs12289252	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12290684	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1540081	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1540082	0.82[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs17211577	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs1894012	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1938924	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1938926	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938928	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1938938	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2032356	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2051433	0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2155035	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2840368	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs4144865	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4944601	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4944604	0.96[ASN][1000 genomes]
rs4944610	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4944613	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs722157	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs722158	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7940587	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7940590	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7940772	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7940781	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7940788	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs949350	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9634021	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv520466	chr11:86344677-86346940	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv555704	chr11:86344677-86386784	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86331000-86346200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:86333200-86349800	Weak transcription	Esophagus	oesophagus
3	chr11:86335600-86345200	Enhancers	NHDF-Ad	bronchial
4	chr11:86336000-86348000	Weak transcription	Fetal Intestine Small	intestine
5	chr11:86339200-86349200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr11:86340000-86357200	Weak transcription	Fetal Brain Female	brain
7	chr11:86341000-86347400	Weak transcription	Fetal Kidney	kidney
8	chr11:86341000-86349000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr11:86341000-86355400	Weak transcription	Adipose Nuclei	Adipose
10	chr11:86341600-86358800	Weak transcription	Brain Anterior Caudate	brain
11	chr11:86342000-86349200	Weak transcription	Fetal Heart	heart
12	chr11:86342200-86348400	Weak transcription	Left Ventricle	heart
13	chr11:86342200-86348400	Weak transcription	Right Ventricle	heart
14	chr11:86342200-86348800	Weak transcription	Brain Angular Gyrus	brain
15	chr11:86342200-86351400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:86342200-86353200	Weak transcription	Aorta	Aorta
17	chr11:86342200-86356400	Weak transcription	Fetal Stomach	stomach
18	chr11:86342600-86347400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr11:86343200-86345000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:86343200-86345000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:86343200-86345000	Enhancers	HUVEC	blood vessel
22	chr11:86343200-86345200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:86343200-86345200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr11:86343200-86345200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr11:86343200-86345400	Enhancers	HSMM	muscle
26	chr11:86343800-86345400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:86343800-86350000	Weak transcription	Colon Smooth Muscle	Colon
28	chr11:86344000-86345400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:86344000-86373800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr11:86344200-86346000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:86344200-86346200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:86344200-86352800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr11:86344400-86345000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:86344400-86345600	Enhancers	A549	lung
35	chr11:86344400-86347000	Weak transcription	Ovary	ovary
36	chr11:86344400-86348400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:86344400-86349000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr11:86344600-86347000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:86344600-86347000	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr11:86344600-86354600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr11:86344800-86345000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:86344800-86345000	Enhancers	Spleen	Spleen
43	chr11:86344800-86346600	Weak transcription	NH-A	brain
44	chr11:86344800-86346800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:86344800-86346800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:86344800-86347000	Weak transcription	NHLF	lung
47	chr11:86344800-86347400	Weak transcription	HMEC	breast
48	chr11:86344800-86348800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:86344800-86349000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:86344800-86349000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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