Variant report

Variant	rs9810077
Chromosome Location	chr3:195005422-195005423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:194990700..194993789-chr3:195004224..195007014,3	MCF-7	breast:
2	chr3:195002020..195004073-chr3:195005404..195007900,2	K562	blood:

Variant related genes	Relation type
ENSG00000173950	Chromatin interaction
ENSG00000229325	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10804414	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1094677	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11706264	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12695049	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13059843	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13062518	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13072826	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13072883	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091924	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13099106	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13324903	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1538767	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2791603	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4677834	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4677835	0.83[EUR][1000 genomes]
rs55672262	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55927338	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6778719	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7611238	0.85[EUR][1000 genomes]
rs7633265	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7634345	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7651757	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs823300	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs823301	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs823302	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs823306	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs823310	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs823311	0.85[ASN][1000 genomes]
rs823314	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9823964	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840346	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9810077	XXYLT1	cis	Skin Sun Exposed Lower leg	GTEx
rs9810077	XXYLT1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194992400-195009000	Weak transcription	Spleen	Spleen
2	chr3:194992600-195008200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:194992600-195008800	Weak transcription	Lung	lung
4	chr3:194992600-195090000	Weak transcription	Aorta	Aorta
5	chr3:194992800-195008600	Weak transcription	Ovary	ovary
6	chr3:194992800-195039800	Weak transcription	Fetal Brain Male	brain
7	chr3:194992800-195039800	Weak transcription	Right Ventricle	heart
8	chr3:194993000-195005600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:194993000-195005600	Weak transcription	HSMM	muscle
10	chr3:194993000-195005600	Weak transcription	HSMMtube	muscle
11	chr3:194993000-195006200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:194993000-195006200	Weak transcription	Brain Anterior Caudate	brain
13	chr3:194993000-195006800	Weak transcription	NHLF	lung
14	chr3:194993000-195007000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:194993000-195007000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:194993000-195007200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:194993000-195007200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:194993000-195008200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:194993000-195008200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:194993000-195008800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:194993000-195009000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:194993000-195009600	Weak transcription	Fetal Kidney	kidney
23	chr3:194993000-195012800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:194993000-195020800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:194993000-195021400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:194993000-195038600	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:194993000-195039200	Weak transcription	Brain Germinal Matrix	brain
28	chr3:194993000-195039600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:194993000-195050400	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:194993000-195076000	Weak transcription	Fetal Heart	heart
31	chr3:194993200-195005600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:194993200-195005800	Weak transcription	HMEC	breast
33	chr3:194993200-195006400	Weak transcription	HUVEC	blood vessel
34	chr3:194993200-195006800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:194993200-195006800	Weak transcription	NHDF-Ad	bronchial
36	chr3:194993200-195007200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:194993200-195013000	Weak transcription	Hela-S3	cervix
38	chr3:194993400-195005800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:194995000-195039800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr3:194995400-195008800	Weak transcription	K562	blood
41	chr3:194995400-195040000	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr3:194996000-195005800	Weak transcription	HepG2	liver
43	chr3:194996200-195032200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:194996400-195033800	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:194996800-195008600	Weak transcription	Brain Angular Gyrus	brain
46	chr3:194997200-195027400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:194997800-195005600	Weak transcription	NH-A	brain
48	chr3:194999200-195029400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr3:194999800-195005600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:194999800-195008200	Weak transcription	Thymus	Thymus

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