Variant report

Variant	rs498342
Chromosome Location	chr19:35713451-35713452
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:35712851..35714718-chr19:35758773..35761081,2	MCF-7	breast:
2	chr19:35710070..35713514-chr19:35713713..35717849,5	K562	blood:
3	chr19:35699047..35700792-chr19:35711759..35713606,2	MCF-7	breast:
4	chr19:35713436..35715934-chr19:35738394..35740561,3	K562	blood:
5	chr19:35711748..35715116-chr19:35794768..35797125,3	K562	blood:
6	chr19:35709723..35716939-chr19:35736912..35742309,9	K562	blood:
7	chr19:35711756..35713558-chr19:35723601..35726403,2	K562	blood:
8	chr19:35712673..35716305-chr19:35736925..35742243,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000105699	Chromatin interaction
ENSG00000262497	Chromatin interaction
ENSG00000105698	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10403023	0.98[ASN][1000 genomes]
rs10425008	0.85[AFR][1000 genomes]
rs10425846	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11084808	0.85[AFR][1000 genomes]
rs12463330	0.84[AFR][1000 genomes]
rs12982723	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1633924	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1688010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1688011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1688012	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17541474	0.88[CEU][hapmap]
rs17613706	0.94[CEU][hapmap]
rs2188328	0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs2214021	0.83[YRI][hapmap];0.88[AFR][1000 genomes]
rs28579145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs495570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534481	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540818	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];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107155	0.80[AFR][1000 genomes]
rs8182468	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv1066553	chr19:35698638-35749563	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	esv2763203	chr19:35700047-35738400	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs498342	THAP8	cis	cerebellum	SCAN
rs498342	TEX101	cis	cerebellum	SCAN
rs498342	DPF1	cis	cerebellum	SCAN
rs498342	SERTAD3	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35705400-35715200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:35706000-35715200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:35707000-35714200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr19:35708000-35713600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:35708000-35714400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr19:35708200-35715000	Weak transcription	Gastric	stomach
7	chr19:35710200-35713600	Enhancers	Primary hematopoietic stem cells	blood
8	chr19:35710200-35717000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:35710600-35717000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:35710800-35715600	Weak transcription	Spleen	Spleen
11	chr19:35711200-35715200	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr19:35711800-35715400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr19:35711800-35715600	Weak transcription	Pancreas	Pancrea
14	chr19:35711800-35716000	Weak transcription	Fetal Heart	heart
15	chr19:35712000-35714200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:35712000-35714200	Weak transcription	Stomach Mucosa	stomach
17	chr19:35712000-35716000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr19:35712800-35714400	Weak transcription	Right Ventricle	heart
19	chr19:35713200-35713600	Enhancers	Primary B cells from cord blood	blood
20	chr19:35713200-35714200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr19:35713200-35714600	ZNF genes & repeats	K562	blood
22	chr19:35713400-35713600	Enhancers	Primary B cells from peripheral blood	blood
23	chr19:35713400-35713600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:35713400-35713600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr19:35713400-35716800	Enhancers	Primary T cells fromperipheralblood	blood

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