Variant report

Variant	rs227418
Chromosome Location	chr14:70459712-70459713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:70456335-70461656	Hela-S3	cervix:	n/a	n/a
2	ZNF263	chr14:70459657-70459992	HEK293-T-REx	kidney:	n/a	chr14:70459820-70459841 chr14:70459772-70459781
3	POLR2A	chr14:70459667-70460803	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr14:70459525-70460954	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr14:70459711-70459937	Hela-S3	cervix:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr14:70459663-70459713	T-47D	breast:	n/a
2	chr14:70459663-70459713	RPTEC	kidney:	n/a
3	chr14:70459663-70459713	Hepatocyte	liver:	n/a
4	chr14:70459663-70459713	NT2-D1	testis:	n/a
5	chr14:70459663-70459713	HMEC	breast:	n/a
6	chr14:70459663-70459713	MCF10A-Er-Src	breast:	n/a
7	chr14:70459663-70459713	PrEC	prostate:	n/a
8	chr14:70459663-70459713	PFSK-1	brain:	n/a
9	chr14:70459663-70459713	ECC-1	luminal epithelium:	n/a
10	chr14:70459663-70459713	GM12892	blood:	n/a
11	chr14:70459663-70459713	AG09309	skin:	n/a
12	chr14:70459663-70459713	SK-N-SH_RA	brain:	n/a
13	chr14:70459663-70459713	Jurkat	blood:	n/a
14	chr14:70459663-70459713	SK-N-MC	brain:	n/a
15	chr14:70459663-70459713	HUVEC	blood vessel:	n/a
16	chr14:70459663-70459713	HPAEpiC	pulmonary alveolar:	n/a
17	chr14:70459663-70459713	NHBE	bronchial:	n/a
18	chr14:70459663-70459713	BE2_C	brain:	n/a
19	chr14:70459663-70459713	HCT-116	colon:	n/a
20	chr14:70459663-70459713	AG04450	lung:	fetal
21	chr14:70459663-70459713	GM06990	blood:	n/a
22	chr14:70459663-70459713	ovcar-3	ovarian:	n/a
23	chr14:70459663-70459713	HepG2	liver:	n/a
24	chr14:70459663-70459713	HRCEpiC	kidney:	n/a
25	chr14:70459663-70459713	HCF	heart:	n/a
26	chr14:70459663-70459713	HAEpiC	amniotic membrane:	n/a
27	chr14:70459663-70459713	Caco-2	colon:	n/a
28	chr14:70459663-70459713	HEEpiC	esophagus:	n/a
29	chr14:70459663-70459713	IMR90	lung:	fetal
30	chr14:70459663-70459713	AG10803	skin:	n/a
31	chr14:70459663-70459713	SAEC	small airway:	n/a
32	chr14:70459663-70459713	GM12891	blood:	n/a
33	chr14:70459663-70459713	SKMC	muscle:	n/a
34	chr14:70459663-70459713	CMK	blood:	n/a
35	chr14:70459663-70459713	MCF-7	breast:	n/a
36	chr14:70459663-70459713	NH-A	brain:	n/a
37	chr14:70459663-70459713	HEK293	kidney:	embryo
38	chr14:70459663-70459713	Hela-S3	cervix:	n/a
39	chr14:70459663-70459713	AG09319	gingival:	n/a
40	chr14:70459663-70459713	NB4	blood:	n/a
41	chr14:70459663-70459713	H1-hESC	embryonic stem cell:	embryo
42	chr14:70459663-70459713	HIPEpiC	eye:	n/a
43	chr14:70459663-70459713	GM19239	blood:	n/a
44	chr14:70459663-70459713	AG04449	skin:	fetal
45	chr14:70459663-70459713	ProgFib	skin:	n/a
46	chr14:70459663-70459713	HCM	heart:	n/a
47	chr14:70459663-70459713	HRE	kidney:	n/a
48	chr14:70459663-70459713	U87	brain:	n/a
49	chr14:70459663-70459713	GM12878	blood:	n/a
50	chr14:70459663-70459713	HL-60	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:70458044..70460070-chr14:70460426..70463447,3	MCF-7	breast:

No data

Variant related genes	Relation type
SMOC1	TF binding region
SMOC1	CpG island
ENSG00000198732	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10130486	1.00[CHB][hapmap]
rs10140220	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10140517	0.96[ASN][1000 genomes]
rs10140592	0.96[ASN][1000 genomes]
rs10140789	0.96[ASN][1000 genomes]
rs11628205	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11844519	0.89[CEU][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs12884121	1.00[CHB][hapmap]
rs1380433	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs170569	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]
rs17107529	0.87[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17107549	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs17107556	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17107580	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs227415	0.89[CEU][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs227421	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]
rs7158909	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456336	chr14:70081956-70574149	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv565007	chr14:70081956-70574149	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv832824	chr14:70320639-70511401	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs227418	SMOC1	cis	cerebellum	SCAN
rs227418	AIRE	trans	cerebellum	SCAN
rs227418	ZFYVE26	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70439800-70477200	Weak transcription	Spleen	Spleen
2	chr14:70450600-70464800	Weak transcription	Fetal Stomach	stomach
3	chr14:70450600-70477200	Weak transcription	Fetal Brain Female	brain
4	chr14:70452800-70460600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr14:70453000-70464800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr14:70453200-70462600	Weak transcription	NHEK	skin
7	chr14:70453600-70462600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:70454800-70460800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr14:70456800-70463800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr14:70456800-70463800	Weak transcription	Pancreas	Pancrea
11	chr14:70457400-70464200	Weak transcription	HepG2	liver
12	chr14:70457800-70484800	Weak transcription	Brain Substantia Nigra	brain
13	chr14:70458400-70464600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:70458600-70463800	Weak transcription	Liver	Liver
15	chr14:70458600-70480800	Weak transcription	Brain Germinal Matrix	brain
16	chr14:70458800-70460400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr14:70458800-70464200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr14:70458800-70465400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr14:70459000-70461400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr14:70459000-70461400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr14:70459000-70484800	Weak transcription	Gastric	stomach
22	chr14:70459200-70460000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr14:70459200-70460000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
24	chr14:70459400-70462200	Genic enhancers	Hela-S3	cervix

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