Variant report

Variant	rs34509804
Chromosome Location	chr19:18520865-18520866
allele	A/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18385043..18394940-chr19:18518893..18533267,53	K562	blood:
2	chr19:18431970..18434104-chr19:18519792..18521568,2	MCF-7	breast:
3	chr19:18495971..18498335-chr19:18520063..18523312,3	MCF-7	breast:
4	chr19:18303468..18305230-chr19:18519611..18522345,2	MCF-7	breast:
5	chr19:18432421..18435381-chr19:18520183..18521909,2	MCF-7	breast:
6	chr19:18383365..18408325-chr19:18518460..18533256,66	K562	blood:
7	chr19:18495627..18501937-chr19:18519170..18524838,12	K562	blood:
8	chr19:18520199..18523408-chr19:18523976..18531789,10	MCF-7	breast:
9	chr19:18391400..18392944-chr19:18520489..18523439,2	MCF-7	breast:
10	chr19:18519965..18521698-chr19:18535153..18537239,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267959	Chromatin interaction
ENSG00000241464	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000130520	Chromatin interaction
ENSG00000254858	Chromatin interaction
ENSG00000264175	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000130518	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10164319	0.83[ASN][1000 genomes]
rs10405479	0.83[ASN][1000 genomes]
rs10405636	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10408290	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10409003	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10409483	0.81[EUR][1000 genomes]
rs10409505	0.81[EUR][1000 genomes]
rs10413237	0.81[EUR][1000 genomes]
rs10425982	0.81[EUR][1000 genomes]
rs10427083	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1043327	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10442	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11673604	0.85[EUR][1000 genomes]
rs1560118	0.83[ASN][1000 genomes]
rs1560119	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1806980	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2007981	0.83[ASN][1000 genomes]
rs2288428	0.82[ASN][1000 genomes]
rs2303695	0.81[ASN][1000 genomes]
rs2303696	0.80[ASN][1000 genomes]
rs2303697	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2385088	0.85[ASN][1000 genomes]
rs28572537	0.83[ASN][1000 genomes]
rs34010330	0.83[ASN][1000 genomes]
rs34053595	0.83[ASN][1000 genomes]
rs34171762	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34746918	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3810429	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4595905	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4808801	0.83[ASN][1000 genomes]
rs7254249	0.81[EUR][1000 genomes]
rs7256534	0.81[EUR][1000 genomes]
rs7257932	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7258465	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs748609	0.83[ASN][1000 genomes]
rs8100767	0.81[EUR][1000 genomes]
rs8103622	0.83[ASN][1000 genomes]
rs8103660	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8106096	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8107367	0.83[ASN][1000 genomes]
rs8107743	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8111708	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
3	esv3323899	chr19:18343484-18620429	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 miRNA	162 gene(s)	inside rSNPs	diseases
4	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv428018	chr19:18454891-18663981	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911275	chr19:18484922-18586759	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
9	nsv911276	chr19:18497141-18554972	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
10	nsv911277	chr19:18520231-18552139	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34509804	SSBP4	cis	Esophagus Mucosa	GTEx
rs34509804	SSBP4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18508400-18525400	Weak transcription	Right Atrium	heart
2	chr19:18508800-18525200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr19:18513000-18525600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr19:18514000-18521200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:18514800-18523600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr19:18515200-18521200	Weak transcription	Fetal Muscle Leg	muscle
7	chr19:18515200-18524800	Weak transcription	A549	lung
8	chr19:18515200-18524800	Weak transcription	HepG2	liver
9	chr19:18515200-18525000	Weak transcription	Fetal Intestine Large	intestine
10	chr19:18516200-18524800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:18517200-18521200	Weak transcription	Placenta	Placenta
12	chr19:18518200-18521400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr19:18519200-18521200	Weak transcription	Fetal Intestine Small	intestine
14	chr19:18519200-18521200	Weak transcription	Fetal Thymus	thymus
15	chr19:18519200-18521200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr19:18519200-18521200	Weak transcription	Osteobl	bone
17	chr19:18519200-18521400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:18519200-18521400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:18519200-18521400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr19:18519200-18521400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr19:18519200-18521400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr19:18519200-18523400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:18519200-18524800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr19:18519200-18524800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:18519400-18521200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:18519400-18521400	Weak transcription	K562	blood
27	chr19:18519400-18525200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr19:18519600-18524800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:18519800-18525000	Weak transcription	GM12878-XiMat	blood
30	chr19:18520400-18525200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:18520600-18525200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:18520800-18521000	Weak transcription	Hela-S3	cervix

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