Variant report

Variant	rs2399427
Chromosome Location	chr3:112107594-112107595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12631437	0.98[ASN][1000 genomes]
rs2244350	0.91[ASN][1000 genomes]
rs2633600	0.96[ASN][1000 genomes]
rs4682403	0.98[ASN][1000 genomes]
rs4682404	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72622325	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877341	chr3:112079277-112125521	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv1002567	chr3:112088498-112144063	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2830128	chr3:112090292-112144026	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv591294	chr3:112091220-112208750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv591295	chr3:112093413-112113334	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1004948	chr3:112098217-112113334	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
7	nsv999904	chr3:112098217-112114816	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
8	nsv1010208	chr3:112098542-112227212	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1011313	chr3:112098993-112113334	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
10	nsv1010410	chr3:112099148-112113334	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
11	nsv997659	chr3:112099148-112135687	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1007459	chr3:112099647-112113334	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
13	nsv1006537	chr3:112099647-112114816	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
14	esv3494206	chr3:112101762-112115260	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	n/a	n/a	inside rSNPs	n/a
15	esv3494204	chr3:112102212-112115110	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	n/a
16	esv2763734	chr3:112102565-112113334	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	n/a
17	nsv1011643	chr3:112102565-112113334	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	n/a
18	nsv1003368	chr3:112102565-112114816	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	n/a
19	nsv1008191	chr3:112102565-112114993	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	n/a	n/a	inside rSNPs	n/a
20	nsv998316	chr3:112102565-112116643	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	lncRNA	n/a	inside rSNPs	n/a
21	esv3463477	chr3:112102780-112114174	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	n/a
22	esv3463478	chr3:112102780-112114174	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a
23	esv3494205	chr3:112102877-112114096	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	n/a
24	esv3494208	chr3:112102877-112114096	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	n/a
25	nsv591296	chr3:112103140-112110022	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a
26	nsv591297	chr3:112103140-112113143	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	n/a
27	nsv591298	chr3:112103140-112113334	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	n/a
28	nsv818165	chr3:112103140-112113334	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	n/a
29	nsv516790	chr3:112103140-112114816	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	n/a
30	nsv591299	chr3:112103140-112114816	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	n/a	n/a	inside rSNPs	n/a
31	nsv997722	chr3:112103509-112114816	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a
32	nsv1011145	chr3:112103509-112114993	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a
33	esv2757004	chr3:112104875-112113334	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	n/a
34	esv2759169	chr3:112104875-112113334	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2399427	C3orf17	cis	Esophagus Muscularis	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112097600-112110400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:112098000-112108800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:112098400-112108800	Weak transcription	NH-A	brain
4	chr3:112098800-112108400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:112098800-112108400	Weak transcription	HMEC	breast
6	chr3:112101800-112110000	Weak transcription	Aorta	Aorta
7	chr3:112103800-112108600	Weak transcription	Osteobl	bone
8	chr3:112104200-112108000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:112104200-112108400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:112104200-112108400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:112104200-112108400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:112104400-112108600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:112104600-112107800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:112104800-112108400	Weak transcription	HUVEC	blood vessel
15	chr3:112105200-112109000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr3:112105600-112108600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:112106600-112109000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:112107000-112108600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr3:112107200-112107600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr3:112107200-112107800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr3:112107200-112108400	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr3:112107200-112108600	Enhancers	Fetal Thymus	thymus
23	chr3:112107200-112109200	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr3:112107200-112110000	Enhancers	Fetal Lung	lung
25	chr3:112107200-112111000	Enhancers	Primary T cells from cord blood	blood
26	chr3:112107200-112111600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:112107200-112114000	Enhancers	Primary hematopoietic stem cells	blood
28	chr3:112107200-112117000	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr3:112107400-112108200	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr3:112107400-112110000	Weak transcription	Thymus	Thymus
31	chr3:112107400-112111600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr3:112107400-112114000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:112107400-112117000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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