Variant report

Variant	rs9823964
Chromosome Location	chr3:195004904-195004905
allele	A/C
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:

Variant related genes	Relation type
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10804414	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1094677	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1105165	1.00[CHB][hapmap]
rs11706264	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12695049	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13059843	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13062518	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13072826	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13072883	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091924	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13099106	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13324903	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1538767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2791603	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4677834	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4677835	0.84[EUR][1000 genomes]
rs55672262	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55927338	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6778719	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7611238	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs7633265	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7634345	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7651757	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs823300	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs823301	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs823302	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs823306	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs823310	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs823311	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs823314	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs931528	0.83[CHB][hapmap]
rs9810077	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840346	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.97[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9823964	XXYLT1	cis	Esophagus Mucosa	GTEx
rs9823964	ACAP2	cis	parietal	SCAN
rs9823964	XXYLT1	cis	Skin Sun Exposed Lower leg	GTEx
rs9823964	ACAP2	cis	cerebellum	SCAN

Chromatin state (count:119 , 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	chr3:194992800-195005400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:194992800-195008600	Weak transcription	Ovary	ovary
7	chr3:194992800-195039800	Weak transcription	Fetal Brain Male	brain
8	chr3:194992800-195039800	Weak transcription	Right Ventricle	heart
9	chr3:194993000-195005000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:194993000-195005200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:194993000-195005600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:194993000-195005600	Weak transcription	HSMM	muscle
13	chr3:194993000-195005600	Weak transcription	HSMMtube	muscle
14	chr3:194993000-195006200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:194993000-195006200	Weak transcription	Brain Anterior Caudate	brain
16	chr3:194993000-195006800	Weak transcription	NHLF	lung
17	chr3:194993000-195007000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:194993000-195007000	Weak transcription	Brain Substantia Nigra	brain
19	chr3:194993000-195007200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:194993000-195007200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:194993000-195008200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:194993000-195008200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:194993000-195008800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:194993000-195009000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:194993000-195009600	Weak transcription	Fetal Kidney	kidney
26	chr3:194993000-195012800	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:194993000-195020800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:194993000-195021400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:194993000-195038600	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:194993000-195039200	Weak transcription	Brain Germinal Matrix	brain
31	chr3:194993000-195039600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:194993000-195050400	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:194993000-195076000	Weak transcription	Fetal Heart	heart
34	chr3:194993200-195005600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:194993200-195005800	Weak transcription	HMEC	breast
36	chr3:194993200-195006400	Weak transcription	HUVEC	blood vessel
37	chr3:194993200-195006800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:194993200-195006800	Weak transcription	NHDF-Ad	bronchial
39	chr3:194993200-195007200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:194993200-195013000	Weak transcription	Hela-S3	cervix
41	chr3:194993400-195005800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:194995000-195039800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:194995400-195008800	Weak transcription	K562	blood
44	chr3:194995400-195040000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr3:194996000-195005800	Weak transcription	HepG2	liver
46	chr3:194996200-195032200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:194996400-195033800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:194996800-195008600	Weak transcription	Brain Angular Gyrus	brain
49	chr3:194997200-195027400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:194997800-195005600	Weak transcription	NH-A	brain

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