Variant report

Variant	rs2856289
Chromosome Location	chr17:18149854-18149855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:18149816-18149932	HUVEC	blood vessel:	n/a	n/a
2	HMGN3	chr17:18149851-18151113	K562	blood:	n/a	n/a
3	POLR2A	chr17:18148185-18151299	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr17:18148222-18150304	HepG2	liver:	n/a	n/a
5	POLR2A	chr17:18148191-18150261	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr17:18148876-18151111	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr17:18148059-18149929	U87	brain:	n/a	n/a
8	POLR2A	chr17:18148192-18150259	A549	lung:	n/a	n/a
9	POLR2A	chr17:18148235-18151037	K562	blood:	n/a	n/a
10	POLR2A	chr17:18148189-18149896	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:18127536..18130433-chr17:18148836..18151541,2	MCF-7	breast:
2	chr17:18149206..18150883-chr17:18160011..18162354,3	K562	blood:
3	chr17:18136077..18142771-chr17:18143654..18157956,22	MCF-7	breast:
4	chr17:18135872..18138183-chr17:18147458..18150169,3	K562	blood:
5	chr17:18128887..18137475-chr17:18144772..18151698,11	K562	blood:
6	chr17:18128446..18130837-chr17:18148104..18152552,6	MCF-7	breast:
7	chr17:18125152..18133137-chr17:18145532..18152012,9	K562	blood:

No data

Variant related genes	Relation type
FLII	TF binding region
ENSG00000131899	Chromatin interaction
ENSG00000177731	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12051649	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2071241	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2075657	0.84[EUR][1000 genomes]
rs2075658	0.80[EUR][1000 genomes]
rs2245430	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2473656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2605133	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4925144	0.81[EUR][1000 genomes]
rs59588957	0.81[EUR][1000 genomes]
rs712271	0.81[EUR][1000 genomes]
rs712274	0.86[EUR][1000 genomes]
rs72831919	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs854773	0.81[EUR][1000 genomes]
rs854774	0.81[EUR][1000 genomes]
rs854778	0.81[EUR][1000 genomes]
rs854780	0.80[EUR][1000 genomes]
rs854783	0.80[EUR][1000 genomes]
rs854800	0.80[EUR][1000 genomes]
rs854802	0.80[EUR][1000 genomes]
rs854803	0.81[EUR][1000 genomes]
rs9899249	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9903403	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9903591	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9913262	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	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
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' 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	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	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
7	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv543246	chr17:18121007-18165604	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
11	nsv9503	chr17:18121474-18169166	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
12	nsv907776	chr17:18122485-18170948	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
13	nsv1066718	chr17:18125122-18180807	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv907777	chr17:18131087-18163262	Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2856289	SHMT1	cis	multi-tissue	Pritchard
rs2856289	SHMT1	cis	Artery Tibial	GTEx
rs2856289	SHMT1	cis	Whole Blood	GTEx
rs2856289	SHMT1	cis	Esophagus Muscularis	GTEx
rs2856289	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs2856289	SHMT1	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18130200-18150800	Weak transcription	Right Atrium	heart
2	chr17:18134600-18150800	Weak transcription	Fetal Brain Male	brain
3	chr17:18134600-18150800	Strong transcription	Fetal Stomach	stomach
4	chr17:18135200-18150000	Strong transcription	Fetal Muscle Leg	muscle
5	chr17:18135200-18150600	Strong transcription	Brain Germinal Matrix	brain
6	chr17:18135200-18160000	Strong transcription	Fetal Brain Female	brain
7	chr17:18135400-18150000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr17:18135400-18150000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr17:18135400-18159600	Strong transcription	Primary T cells from cord blood	blood
10	chr17:18135400-18160200	Strong transcription	Thymus	Thymus
11	chr17:18135600-18150600	Strong transcription	Adipose Nuclei	Adipose
12	chr17:18135600-18159000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:18135600-18159400	Strong transcription	Fetal Lung	lung
14	chr17:18135600-18160000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr17:18135800-18150000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:18135800-18150600	Strong transcription	Stomach Smooth Muscle	stomach
17	chr17:18135800-18160400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:18136000-18150000	Strong transcription	Ovary	ovary
19	chr17:18136000-18159800	Strong transcription	Placenta Amnion	Placenta Amnion
20	chr17:18136000-18160000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr17:18136200-18150800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr17:18136200-18160000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr17:18136200-18160000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr17:18137000-18150600	Strong transcription	Brain Anterior Caudate	brain
25	chr17:18137000-18151000	Strong transcription	Brain Cingulate Gyrus	brain
26	chr17:18139400-18150600	Strong transcription	Brain Angular Gyrus	brain
27	chr17:18139400-18150600	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr17:18139400-18159800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr17:18139600-18150400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr17:18139600-18150800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr17:18139800-18160000	Strong transcription	Osteobl	bone
32	chr17:18139800-18160200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr17:18140000-18150000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr17:18140000-18150200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr17:18140000-18160000	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr17:18140400-18150600	Strong transcription	Brain Substantia Nigra	brain
37	chr17:18140800-18150600	Strong transcription	Brain Hippocampus Middle	brain
38	chr17:18143200-18150000	Strong transcription	Colonic Mucosa	Colon
39	chr17:18143400-18160200	Strong transcription	NHLF	lung
40	chr17:18143600-18150600	Strong transcription	Right Ventricle	heart
41	chr17:18143600-18160000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr17:18143800-18150000	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr17:18143800-18150600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr17:18143800-18150600	Weak transcription	Fetal Heart	heart
45	chr17:18143800-18160000	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr17:18143800-18160200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr17:18144000-18150600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:18144000-18150800	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr17:18144000-18160000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr17:18144000-18160200	Strong transcription	Primary monocytes fromperipheralblood	blood

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