Variant report

Variant	rs62285259
Chromosome Location	chr3:194991022-194991023
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:194989426..194991874-chr3:195268477..195270198,3	MCF-7	breast:
2	chr3:194990164..194994201-chr3:195268703..195270348,3	K562	blood:
3	chr3:194989462..194991407-chr3:195163007..195164718,2	MCF-7	breast:
4	chr3:194990005..194994037-chr3:194997788..195001012,5	K562	blood:
5	chr3:194990825..194992800-chr3:195162290..195164935,2	K562	blood:
6	chr3:194979343..194985907-chr3:194989595..194992143,7	K562	blood:
7	chr3:194989967..194994399-chr3:195244037..195248390,6	K562	blood:
8	chr3:194990296..194992305-chr3:195248848..195251348,4	MCF-7	breast:
9	chr3:194979343..194983092-chr3:194989595..194993137,5	K562	blood:
10	chr3:194990545..194994377-chr3:195246139..195250306,5	K562	blood:
11	chr3:194990474..194992109-chr3:195269592..195271685,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000252620	Chromatin interaction
ENSG00000184203	Chromatin interaction
ENSG00000173950	Chromatin interaction
ENSG00000114331	Chromatin interaction
ENSG00000223711	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10933704	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11706218	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11709417	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11715185	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11715202	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12054333	0.82[AMR][1000 genomes]
rs12054406	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12630009	0.82[AMR][1000 genomes]
rs2000051	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2000052	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2066154	0.80[ASN][1000 genomes]
rs2275519	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2410804	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4461369	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4677666	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4677668	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4677669	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4677826	0.82[AMR][1000 genomes]
rs4677829	0.80[ASN][1000 genomes]
rs57124286	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59563484	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60042817	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62287061	0.97[AFR][1000 genomes]
rs62287066	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62287069	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62287106	0.80[ASN][1000 genomes]
rs62287107	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62287108	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62287109	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6437471	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7611090	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7618499	0.81[AMR][1000 genomes]
rs7622180	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7632534	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7641810	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7652612	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7653406	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9790153	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
5	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
6	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
7	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
12	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
13	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
14	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
15	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
16	esv1818370	chr3:194987569-194995096	Flanking Active TSS Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
17	esv1818606	chr3:194987569-194995096	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
18	nsv592983	chr3:194987569-194995096	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
19	nsv592984	chr3:194990363-194991844	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62285259	XXYLT1	cis	Skin Sun Exposed Lower leg	GTEx
rs62285259	XXYLT1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194981800-194991200	Weak transcription	Small Intestine	intestine
2	chr3:194989400-194991200	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr3:194990000-194991200	Flanking Active TSS	Fetal Brain Female	brain
4	chr3:194990000-194991200	Flanking Active TSS	GM12878-XiMat	blood
5	chr3:194990000-194991400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:194990000-194991400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:194990000-194991400	Flanking Active TSS	Dnd41	blood
8	chr3:194990000-194991600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr3:194990200-194991200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr3:194990200-194991200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:194990200-194991200	Flanking Active TSS	Rectal Smooth Muscle	rectum
12	chr3:194990200-194991400	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr3:194990200-194991600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:194990400-194991200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:194990400-194991200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:194990400-194991200	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr3:194990400-194991200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr3:194990400-194991200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:194990400-194991200	Flanking Active TSS	Brain Hippocampus Middle	brain
20	chr3:194990400-194991200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr3:194990400-194991200	Flanking Active TSS	HMEC	breast
22	chr3:194990400-194991200	Flanking Active TSS	HSMM	muscle
23	chr3:194990400-194991400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr3:194990400-194991400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
25	chr3:194990400-194991400	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr3:194990400-194991400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr3:194990400-194991600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr3:194990400-194991600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:194990400-194991600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:194990400-194993000	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr3:194990600-194991200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:194990600-194991200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr3:194990600-194991200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr3:194990600-194991200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr3:194990600-194991200	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr3:194990600-194991200	Flanking Active TSS	Fetal Stomach	stomach
37	chr3:194990600-194991400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr3:194990600-194991400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr3:194990600-194991400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr3:194990600-194991400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:194990600-194991400	Flanking Active TSS	Fetal Muscle Trunk	muscle
42	chr3:194990600-194991400	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr3:194990600-194991400	Flanking Active TSS	Fetal Thymus	thymus
44	chr3:194990600-194991400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr3:194990600-194991600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr3:194990600-194991600	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr3:194990600-194991600	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr3:194990600-194991600	Flanking Active TSS	Liver	Liver
49	chr3:194990600-194991600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr3:194990600-194992600	Active TSS	H9 Cell Line	embryonic stem cell

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