Variant report

Variant	rs12695049
Chromosome Location	chr3:194988940-194988941
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	chr3:194986029..194989766-chr3:194990279..194993841,6	K562	blood:
2	chr3:194851287..194852978-chr3:194986422..194989063,2	K562	blood:

Variant related genes	Relation type
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10804414	0.84[ASN][1000 genomes]
rs1094677	0.84[ASN][1000 genomes]
rs11706264	0.80[ASN][1000 genomes]
rs13059843	0.84[ASN][1000 genomes]
rs13062518	0.84[ASN][1000 genomes]
rs13072883	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13091924	0.84[ASN][1000 genomes]
rs13099106	0.87[ASN][1000 genomes]
rs13324903	0.83[ASN][1000 genomes]
rs1538767	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2791603	0.83[ASN][1000 genomes]
rs4677834	0.84[ASN][1000 genomes]
rs55672262	0.84[ASN][1000 genomes]
rs55927338	0.84[ASN][1000 genomes]
rs6778719	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7633265	0.84[ASN][1000 genomes]
rs7634345	0.84[ASN][1000 genomes]
rs823300	0.84[ASN][1000 genomes]
rs823301	0.84[ASN][1000 genomes]
rs823302	0.84[ASN][1000 genomes]
rs823306	0.82[ASN][1000 genomes]
rs823310	0.84[ASN][1000 genomes]
rs823311	0.83[ASN][1000 genomes]
rs823314	0.84[ASN][1000 genomes]
rs9810077	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9823964	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9840346	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12695049	XXYLT1	cis	Esophagus Mucosa	GTEx
rs12695049	XXYLT1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194981400-194990000	Weak transcription	HSMMtube	muscle
2	chr3:194981400-194990800	Weak transcription	Aorta	Aorta
3	chr3:194981600-194989600	Weak transcription	Right Ventricle	heart
4	chr3:194981600-194989800	Weak transcription	Brain Substantia Nigra	brain
5	chr3:194981600-194990000	Weak transcription	A549	lung
6	chr3:194981600-194990200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:194981600-194990200	Weak transcription	HSMM	muscle
8	chr3:194981600-194990600	Weak transcription	Ovary	ovary
9	chr3:194981800-194989400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:194981800-194989400	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:194981800-194989400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:194981800-194989600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:194981800-194989600	Weak transcription	Liver	Liver
14	chr3:194981800-194989600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:194981800-194989600	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:194981800-194989600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:194981800-194989600	Weak transcription	Fetal Heart	heart
18	chr3:194981800-194989600	Weak transcription	Lung	lung
19	chr3:194981800-194989600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:194981800-194989800	Weak transcription	Adipose Nuclei	Adipose
21	chr3:194981800-194989800	Weak transcription	Colonic Mucosa	Colon
22	chr3:194981800-194989800	Weak transcription	Fetal Brain Female	brain
23	chr3:194981800-194989800	Weak transcription	Gastric	stomach
24	chr3:194981800-194989800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:194981800-194989800	Weak transcription	NHDF-Ad	bronchial
26	chr3:194981800-194990000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:194981800-194990000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:194981800-194990000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:194981800-194990000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:194981800-194990000	Weak transcription	Brain Anterior Caudate	brain
31	chr3:194981800-194990000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:194981800-194990000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:194981800-194990000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:194981800-194990200	Weak transcription	Fetal Lung	lung
35	chr3:194981800-194990200	Weak transcription	Right Atrium	heart
36	chr3:194981800-194990200	Weak transcription	NH-A	brain
37	chr3:194981800-194990200	Weak transcription	Osteobl	bone
38	chr3:194981800-194990400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:194981800-194990400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:194981800-194990400	Weak transcription	Thymus	Thymus
41	chr3:194981800-194991200	Weak transcription	Small Intestine	intestine
42	chr3:194982000-194989800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:194982200-194989400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:194982200-194989600	Weak transcription	Fetal Brain Male	brain
45	chr3:194982200-194989600	Weak transcription	Placenta	Placenta
46	chr3:194982400-194989400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:194982400-194989600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr3:194982400-194989600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:194982400-194989600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:194982400-194989800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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