Variant report

Variant	rs6493893
Chromosome Location	chr15:57113881-57113882
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57106197..57110196-chr15:57111997..57118015,6	K562	blood:
2	chr15:57107595..57111663-chr15:57111716..57115001,4	K562	blood:
3	chr15:57113666..57114534-chr15:57505943..57506509,2	K562	blood:
4	chr15:57113632..57114331-chr15:57161502..57162048,2	K562	blood:
5	chr15:57112037..57114101-chr15:57115817..57118029,2	K562	blood:
6	chr15:56788456..56789162-chr15:57113822..57114589,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1012321	0.88[EUR][1000 genomes]
rs10450961	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10518878	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10851612	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs1115019	0.94[CEU][hapmap];0.89[TSI][hapmap]
rs11855646	0.85[EUR][1000 genomes]
rs11858368	0.86[EUR][1000 genomes]
rs13379960	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1430819	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1441235	0.81[EUR][1000 genomes]
rs1441236	1.00[CEU][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1612205	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1647378	0.97[ASN][1000 genomes]
rs1647392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657922	0.94[CEU][hapmap];0.82[TSI][hapmap]
rs1657930	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1657934	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657935	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657936	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657937	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657938	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1657939	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1660948	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1660950	0.86[ASN][1000 genomes]
rs1660951	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1660961	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16977079	0.83[ASN][1000 genomes]
rs1967352	0.90[EUR][1000 genomes]
rs1967353	0.88[EUR][1000 genomes]
rs2161933	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2163369	0.91[EUR][1000 genomes]
rs2278613	0.87[CEU][hapmap]
rs2414487	0.85[EUR][1000 genomes]
rs28371400	0.85[EUR][1000 genomes]
rs28468978	0.87[EUR][1000 genomes]
rs28568712	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28609621	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28736360	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28874022	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4313751	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4774893	0.99[ASN][1000 genomes]
rs4774895	0.99[ASN][1000 genomes]
rs56965085	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493886	0.82[CEU][hapmap]
rs6493892	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6493894	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67114210	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67278720	0.82[EUR][1000 genomes]
rs67622899	0.88[EUR][1000 genomes]
rs68083905	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7163302	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7166876	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7175191	0.94[CEU][hapmap];0.89[TSI][hapmap]
rs7178196	0.82[ASN][1000 genomes]
rs7182691	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72747165	0.87[EUR][1000 genomes]
rs7359253	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026149	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8040866	0.91[EUR][1000 genomes]
rs8042606	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9919955	0.88[AMR][1000 genomes];0.83[EUR][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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv569576	chr15:57012816-57126917	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv833020	chr15:57055947-57216068	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv457162	chr15:57083006-57225766	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv569577	chr15:57083006-57225766	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6493893	MNS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57100200-57114000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr15:57105000-57114000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr15:57105000-57114200	Weak transcription	Ovary	ovary
4	chr15:57109400-57114200	Weak transcription	Brain Angular Gyrus	brain
5	chr15:57109400-57114200	Weak transcription	Fetal Kidney	kidney
6	chr15:57109800-57114200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:57109800-57114200	Weak transcription	A549	lung
8	chr15:57110000-57114000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:57110000-57114000	Weak transcription	NHLF	lung
10	chr15:57110000-57114200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:57110000-57114200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:57110000-57114200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr15:57110000-57114200	Weak transcription	Fetal Stomach	stomach
14	chr15:57110000-57114200	Weak transcription	Right Atrium	heart
15	chr15:57110000-57114200	Weak transcription	NHEK	skin
16	chr15:57110000-57118600	Weak transcription	Aorta	Aorta
17	chr15:57110000-57138600	Weak transcription	Left Ventricle	heart
18	chr15:57110200-57114200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:57110200-57114200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:57110200-57114200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr15:57110400-57114000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:57110400-57114200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:57110400-57114200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:57110400-57114200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:57110400-57114200	Weak transcription	HMEC	breast
26	chr15:57110400-57114200	Weak transcription	HSMM	muscle
27	chr15:57110600-57114200	Weak transcription	Fetal Lung	lung
28	chr15:57110600-57114200	Weak transcription	NH-A	brain
29	chr15:57110600-57114200	Weak transcription	NHDF-Ad	bronchial
30	chr15:57110600-57114200	Weak transcription	Osteobl	bone
31	chr15:57110600-57114600	Weak transcription	Fetal Brain Male	brain
32	chr15:57110800-57114200	Weak transcription	Brain Germinal Matrix	brain
33	chr15:57111600-57114600	Enhancers	Fetal Thymus	thymus
34	chr15:57112400-57114600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr15:57112600-57114000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:57112600-57114000	Weak transcription	HSMMtube	muscle
37	chr15:57112600-57116600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:57112800-57114200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:57113000-57130400	Weak transcription	Thymus	Thymus
40	chr15:57113400-57114600	Enhancers	Psoas Muscle	Psoas
41	chr15:57113600-57114400	Enhancers	Adipose Nuclei	Adipose
42	chr15:57113600-57114600	Enhancers	Brain Hippocampus Middle	brain
43	chr15:57113600-57114600	Enhancers	Fetal Muscle Leg	muscle
44	chr15:57113800-57114600	Enhancers	Brain Anterior Caudate	brain
45	chr15:57113800-57114600	Enhancers	Brain Substantia Nigra	brain
46	chr15:57113800-57114600	Enhancers	Colon Smooth Muscle	Colon
47	chr15:57113800-57115000	Enhancers	Fetal Heart	heart

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