Variant report

Variant	rs2399428
Chromosome Location	chr3:112109171-112109172
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1032239	0.94[ASN][1000 genomes]
rs13062867	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13078806	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13093653	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1488264	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2078116	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2633602	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2633603	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2633604	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2633605	0.98[ASN][1000 genomes]
rs2683900	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2683905	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34257022	0.99[ASN][1000 genomes]
rs35938155	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682402	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs57756138	0.98[ASN][1000 genomes]
rs7610866	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7644713	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9647327	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878780	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

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112097600-112110400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:112101800-112110000	Weak transcription	Aorta	Aorta
3	chr3:112107200-112109200	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr3:112107200-112110000	Enhancers	Fetal Lung	lung
5	chr3:112107200-112111000	Enhancers	Primary T cells from cord blood	blood
6	chr3:112107200-112111600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:112107200-112114000	Enhancers	Primary hematopoietic stem cells	blood
8	chr3:112107200-112117000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:112107400-112110000	Weak transcription	Thymus	Thymus
10	chr3:112107400-112111600	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr3:112107400-112114000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:112107400-112117000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:112107600-112109600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr3:112107600-112110000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:112107800-112109600	Enhancers	Brain Cingulate Gyrus	brain
16	chr3:112107800-112109800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr3:112107800-112109800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:112107800-112109800	Weak transcription	Adipose Nuclei	Adipose
19	chr3:112107800-112109800	Enhancers	Brain Anterior Caudate	brain
20	chr3:112107800-112109800	Enhancers	Brain Substantia Nigra	brain
21	chr3:112108000-112109200	Enhancers	H9 Cell Line	embryonic stem cell
22	chr3:112108000-112109200	Enhancers	Brain Hippocampus Middle	brain
23	chr3:112108000-112109600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:112108000-112109800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:112108000-112109800	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:112108000-112110800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:112108000-112110800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:112108200-112109600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:112108200-112110200	Weak transcription	Ovary	ovary
30	chr3:112108200-112111400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr3:112108400-112109200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr3:112108400-112109600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:112108400-112109600	Enhancers	HSMM	muscle
34	chr3:112108400-112109800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:112108400-112109800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:112108400-112109800	Enhancers	HUVEC	blood vessel
37	chr3:112108400-112110000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:112108400-112110200	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr3:112108400-112111000	Enhancers	Placenta	Placenta
40	chr3:112108400-112111200	Enhancers	HMEC	breast
41	chr3:112108400-112111400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:112108600-112109600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:112108600-112109800	Weak transcription	Fetal Thymus	thymus
44	chr3:112108600-112109800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:112108600-112110000	Enhancers	Osteobl	bone
46	chr3:112108600-112110200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:112108600-112110800	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr3:112108600-112110800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:112108600-112110800	Enhancers	NHEK	skin
50	chr3:112108600-112111000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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