Variant report

Variant	rs35088354
Chromosome Location	chr19:56108735-56108736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:55986000..55989537-chr19:56108522..56112833,7	MCF-7	breast:
2	chr19:56046531..56048112-chr19:56108698..56111511,2	MCF-7	breast:
3	chr19:56107031..56108826-chr19:56115985..56118157,2	K562	blood:
4	chr19:56087628..56093963-chr19:56108517..56113906,9	MCF-7	breast:
5	chr19:56107792..56111497-chr19:56151607..56154571,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171425	Chromatin interaction
ENSG00000187550	Chromatin interaction
ENSG00000218891	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000197483	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000267730	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10403432	0.80[ASN][1000 genomes]
rs10403462	0.94[ASN][1000 genomes]
rs10451452	1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs1079082	0.82[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1079083	0.82[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1079084	0.82[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs1079085	0.87[ASN][1000 genomes]
rs11084402	0.82[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs11665826	0.88[ASN][1000 genomes]
rs11668725	0.86[ASN][1000 genomes]
rs11668729	0.86[ASN][1000 genomes]
rs11669682	0.88[ASN][1000 genomes]
rs11879347	0.82[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs12610510	0.82[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs12610512	0.86[ASN][1000 genomes]
rs12610709	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12610881	0.90[ASN][1000 genomes]
rs12972159	0.88[ASN][1000 genomes]
rs12974617	0.85[ASN][1000 genomes]
rs12978375	0.86[ASN][1000 genomes]
rs12979354	0.88[ASN][1000 genomes]
rs12979366	0.88[ASN][1000 genomes]
rs12980543	0.88[ASN][1000 genomes]
rs2161456	0.87[ASW][hapmap];0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes]
rs2864433	0.88[ASN][1000 genomes]
rs2902748	0.88[ASN][1000 genomes]
rs34174244	0.88[ASN][1000 genomes]
rs34715654	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34937940	0.85[ASN][1000 genomes]
rs35197282	0.88[ASN][1000 genomes]
rs35522245	0.88[ASN][1000 genomes]
rs35839536	0.88[ASN][1000 genomes]
rs36047579	0.84[ASN][1000 genomes]
rs60220392	0.88[ASN][1000 genomes]
rs71368855	0.86[ASN][1000 genomes]
rs71368856	0.86[ASN][1000 genomes]
rs7246944	0.83[ASN][1000 genomes]
rs7251733	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer 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	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv912495	chr19:56033088-56132661	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
9	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv912499	chr19:56071293-56132487	Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
12	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
13	nsv912502	chr19:56099884-56138575	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35088354	ZNF304	cis	parietal	SCAN
rs35088354	ZNF671	cis	cerebellum	SCAN
rs35088354	AURKC	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56098800-56109800	Weak transcription	Fetal Heart	heart
2	chr19:56099200-56110000	Weak transcription	Right Atrium	heart
3	chr19:56099800-56110000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:56099800-56110400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:56100000-56109800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr19:56102000-56109800	Strong transcription	Fetal Stomach	stomach
7	chr19:56102600-56109200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr19:56102600-56109200	Strong transcription	Fetal Brain Female	brain
9	chr19:56102600-56109200	Strong transcription	Fetal Thymus	thymus
10	chr19:56102600-56109800	Strong transcription	Fetal Intestine Small	intestine
11	chr19:56102800-56109000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:56102800-56109000	Strong transcription	Primary T cells from cord blood	blood
13	chr19:56102800-56109000	Strong transcription	Brain Cingulate Gyrus	brain
14	chr19:56102800-56109000	Strong transcription	Placenta	Placenta
15	chr19:56102800-56109000	Strong transcription	Ovary	ovary
16	chr19:56102800-56109200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:56102800-56109200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:56102800-56109200	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:56102800-56109200	Strong transcription	Adipose Nuclei	Adipose
20	chr19:56102800-56109200	Strong transcription	Fetal Intestine Large	intestine
21	chr19:56102800-56109200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr19:56102800-56109400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr19:56102800-56109600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:56102800-56110600	Weak transcription	Stomach Mucosa	stomach
25	chr19:56103000-56109000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:56103000-56109000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr19:56103000-56109200	Strong transcription	Liver	Liver
28	chr19:56103000-56109200	Strong transcription	Thymus	Thymus
29	chr19:56103000-56109400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:56103000-56109600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:56103000-56109600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr19:56103200-56109600	Weak transcription	Brain Substantia Nigra	brain
33	chr19:56103400-56108800	Strong transcription	Primary B cells from peripheral blood	blood
34	chr19:56103400-56108800	Strong transcription	A549	lung
35	chr19:56103400-56109000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:56103400-56109000	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:56103400-56109000	Strong transcription	Spleen	Spleen
38	chr19:56103400-56109200	Strong transcription	Left Ventricle	heart
39	chr19:56103400-56109200	Strong transcription	Pancreas	Pancrea
40	chr19:56103400-56109200	Strong transcription	Dnd41	blood
41	chr19:56103400-56109600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:56103400-56109600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:56103600-56109000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:56103600-56109200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:56103600-56109200	Strong transcription	Lung	lung
46	chr19:56103600-56109400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:56103600-56109800	Strong transcription	NHLF	lung
48	chr19:56104800-56110000	Strong transcription	NHEK	skin
49	chr19:56105000-56108800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:56105000-56108800	Strong transcription	Rectal Mucosa Donor 29	rectum

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