Variant report

Variant	rs6430430
Chromosome Location	chr2:134325809-134325810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10200825	0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13401160	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13426165	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16826729	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2123085	1.00[ASW][hapmap]
rs56861595	1.00[AMR][1000 genomes]
rs58896894	1.00[AMR][1000 genomes]
rs60303968	1.00[AMR][1000 genomes]
rs60532004	1.00[AMR][1000 genomes]
rs60818895	1.00[AMR][1000 genomes]
rs6719987	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72992312	1.00[AMR][1000 genomes]
rs72994285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72994288	1.00[AMR][1000 genomes]
rs72996138	1.00[AMR][1000 genomes]
rs73001188	1.00[AMR][1000 genomes]
rs73003129	1.00[AMR][1000 genomes]
rs7576744	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7584046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv516644	chr2:134301130-134391214	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv431713	chr2:134316522-134413604	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1013713	chr2:134322236-134644574	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv535931	chr2:134322236-134644574	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6430430	HNMT	trans	lymphoblastoid	seeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134323800-134326400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr2:134324000-134326400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:134324200-134326400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr2:134324200-134326400	Enhancers	HMEC	breast
5	chr2:134324400-134326400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:134324400-134326400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:134324400-134326400	Active TSS	Fetal Brain Female	brain
8	chr2:134324400-134326400	Flanking Active TSS	NH-A	brain
9	chr2:134324400-134326400	Flanking Active TSS	Osteobl	bone
10	chr2:134324400-134327000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:134324400-134327200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:134324400-134329000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr2:134324600-134326400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:134324600-134326400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr2:134324600-134328600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr2:134324600-134329600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr2:134324600-134330400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:134324800-134326200	Active TSS	Brain Cingulate Gyrus	brain
19	chr2:134324800-134326200	Active TSS	Fetal Intestine Large	intestine
20	chr2:134324800-134326200	Active TSS	Left Ventricle	heart
21	chr2:134324800-134326200	Bivalent Enhancer	HepG2	liver
22	chr2:134324800-134326400	Active TSS	Right Atrium	heart
23	chr2:134324800-134326400	Active TSS	Right Ventricle	heart
24	chr2:134324800-134326600	Active TSS	Brain Anterior Caudate	brain
25	chr2:134325000-134326000	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr2:134325000-134326200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:134325000-134326400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:134325000-134326400	Flanking Active TSS	Fetal Lung	lung
29	chr2:134325000-134326400	Active TSS	Fetal Muscle Trunk	muscle
30	chr2:134325000-134330000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:134325000-134342400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:134325200-134326200	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr2:134325200-134326400	Active TSS	NHDF-Ad	bronchial
34	chr2:134325200-134329000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:134325400-134326000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:134325400-134326000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:134325400-134326000	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr2:134325400-134326000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr2:134325400-134326200	Active TSS	Brain Hippocampus Middle	brain
40	chr2:134325400-134326200	Flanking Active TSS	Fetal Intestine Small	intestine
41	chr2:134325400-134326200	Active TSS	Stomach Mucosa	stomach
42	chr2:134325400-134326200	Flanking Active TSS	HUVEC	blood vessel
43	chr2:134325400-134326400	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr2:134325400-134331800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:134325600-134326000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr2:134325600-134326000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:134325600-134326000	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:134325600-134326000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr2:134325600-134326000	Flanking Active TSS	Fetal Heart	heart
50	chr2:134325600-134326000	Flanking Active TSS	Rectal Smooth Muscle	rectum

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