Variant report

Variant	rs672356
Chromosome Location	chr17:18266567-18266568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18149918..18152295-chr17:18264840..18266898,2	MCF-7	breast:
2	chr17:18217812..18219938-chr17:18264805..18267202,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176994	Chromatin interaction
ENSG00000177302	Chromatin interaction
ENSG00000177731	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11870126	0.80[AMR][1000 genomes]
rs12936769	0.80[AMR][1000 genomes]
rs12937300	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12939092	0.93[EUR][1000 genomes]
rs12939757	0.84[AMR][1000 genomes]
rs12952556	0.81[EUR][1000 genomes]
rs12952667	0.81[EUR][1000 genomes]
rs1563631	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1979277	0.81[EUR][1000 genomes]
rs2230154	0.82[AMR][1000 genomes]
rs2273028	0.83[EUR][1000 genomes]
rs2386456	0.82[AMR][1000 genomes]
rs2461837	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2461838	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3783	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3794772	0.83[EUR][1000 genomes]
rs4632181	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4924750	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4924845	0.80[EUR][1000 genomes]
rs4924847	0.81[EUR][1000 genomes]
rs4924849	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4925171	0.81[EUR][1000 genomes]
rs643333	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6502646	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6502649	0.82[EUR][1000 genomes]
rs7207306	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7222684	0.81[EUR][1000 genomes]
rs8070633	0.82[EUR][1000 genomes]
rs8073464	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8080966	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs921866	0.81[EUR][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	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
9	esv2758443	chr17:18234525-18446384	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
10	esv2758677	chr17:18234525-18446384	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	esv1829832	chr17:18235992-18405148	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
12	nsv827913	chr17:18253785-18572122	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	nsv1065708	chr17:18259174-18913343	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs672356	LGALS9C	cis	Whole Blood	GTEx
rs672356	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs672356	SHMT1	cis	Muscle Skeletal	GTEx
rs672356	SHMT1	cis	Esophagus Muscularis	GTEx
rs672356	SHMT1	cis	multi-tissue	Pritchard
rs672356	SHMT1	cis	Whole Blood	GTEx
rs672356	LLGL1	cis	Esophagus Mucosa	GTEx
rs672356	SHMT1	cis	Artery Aorta	GTEx
rs672356	RP11-258F1.1	cis	Esophagus Muscularis	GTEx
rs672356	ALKBH5	cis	Esophagus Muscularis	GTEx
rs672356	SHMT1	cis	Nerve Tibial	GTEx
rs672356	SHMT1	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18264200-18266800	Active TSS	Liver	Liver
2	chr17:18265200-18266600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr17:18265200-18266600	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr17:18265200-18266800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr17:18265200-18267000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr17:18265200-18267000	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr17:18265200-18267200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr17:18265200-18267200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr17:18265200-18267400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:18265400-18267000	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr17:18265400-18267000	Active TSS	Fetal Kidney	kidney
12	chr17:18265400-18267200	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr17:18265400-18267200	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr17:18265400-18267400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr17:18265600-18266600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr17:18265600-18267000	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr17:18265600-18267000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr17:18265600-18267000	Active TSS	Brain Cingulate Gyrus	brain
19	chr17:18265600-18267000	Active TSS	HMEC	breast
20	chr17:18265600-18267200	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr17:18265600-18267200	Active TSS	A549	lung
22	chr17:18265800-18266600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr17:18265800-18266600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr17:18265800-18266800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr17:18265800-18267000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr17:18265800-18267000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr17:18265800-18267000	Active TSS	Esophagus	oesophagus
28	chr17:18265800-18267000	Active TSS	Rectal Smooth Muscle	rectum
29	chr17:18265800-18267200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr17:18265800-18267200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr17:18265800-18267200	Active TSS	Brain Substantia Nigra	brain
32	chr17:18265800-18267200	Active TSS	NHDF-Ad	bronchial
33	chr17:18265800-18267400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr17:18265800-18267400	Active TSS	Hela-S3	cervix
35	chr17:18265800-18267600	Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr17:18266000-18266600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr17:18266000-18266600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr17:18266000-18266600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr17:18266000-18266600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr17:18266000-18266600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr17:18266000-18266600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr17:18266000-18266600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr17:18266000-18266600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr17:18266000-18266600	Flanking Active TSS	Fetal Muscle Trunk	muscle
45	chr17:18266000-18266600	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr17:18266000-18266600	Flanking Active TSS	Placenta	Placenta
47	chr17:18266000-18266600	Flanking Active TSS	Pancreas	Pancrea
48	chr17:18266000-18266600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr17:18266000-18266600	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr17:18266000-18266600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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