Variant report

Variant	rs638416
Chromosome Location	chr17:18266975-18266976
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr17:18266684-18266997	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr17:18266382-18267167	Hela-S3	cervix:	n/a	n/a
3	YY1	chr17:18266615-18266994	K562	blood:	n/a	chr17:18266707-18266721 chr17:18266867-18266876 chr17:18266706-18266715 chr17:18266628-18266637
4	E2F6	chr17:18266489-18267156	A549	lung:	n/a	chr17:18266707-18266717 chr17:18266806-18266814 chr17:18266867-18266876
5	POLR2A	chr17:18266476-18267243	HUVEC	blood vessel:	n/a	n/a
6	MAX	chr17:18265999-18267224	Hela-S3	cervix:	n/a	chr17:18266762-18266778 chr17:18266770-18266781 chr17:18266771-18266780 chr17:18266771-18266780
7	TAF1	chr17:18266331-18267145	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr17:18266427-18267231	GM12892	blood:	n/a	n/a
9	HCFC1	chr17:18265849-18267418	Hela-S3	cervix:	n/a	n/a
10	USF1	chr17:18266400-18267052	A549	lung:	n/a	chr17:18266498-18266514 chr17:18266949-18266965 chr17:18266562-18266578
11	SIN3A	chr17:18265943-18267245	H1-hESC	embryonic stem cell:	n/a	chr17:18266500-18266511 chr17:18266772-18266781 chr17:18266770-18266779 chr17:18266753-18266764
12	POLR2A	chr17:18266499-18267199	GM19193	blood:	n/a	n/a
13	TAF1	chr17:18266465-18267169	HepG2	liver:	n/a	n/a
14	MAX	chr17:18266032-18267124	A549	lung:	n/a	chr17:18266762-18266778 chr17:18266770-18266781 chr17:18266771-18266780 chr17:18266771-18266780
15	E2F6	chr17:18266579-18267040	K562	blood:	n/a	chr17:18266707-18266717 chr17:18266806-18266814 chr17:18266867-18266876
16	TCF7L2	chr17:18265898-18267134	Hela-S3	cervix:	n/a	n/a
17	NFYA	chr17:18266608-18267116	Hela-S3	cervix:	n/a	chr17:18266880-18266894
18	USF1	chr17:18266465-18267076	A549	lung:	n/a	chr17:18266498-18266514 chr17:18266949-18266965 chr17:18266562-18266578
19	PAX5	chr17:18266605-18267059	GM12878	blood:	n/a	chr17:18266894-18266912
20	POLR2A	chr17:18266415-18267264	ECC-1	luminal epithelium:	n/a	n/a
21	ELF1	chr17:18266704-18267152	HepG2	liver:	n/a	chr17:18266749-18266761 chr17:18266706-18266715 chr17:18266874-18266883
22	MAZ	chr17:18266647-18267441	GM12878	blood:	n/a	chr17:18266762-18266778 chr17:18266770-18266781 chr17:18266771-18266780 chr17:18266771-18266780
23	PML	chr17:18266426-18267221	GM12878	blood:	n/a	n/a
24	USF1	chr17:18266269-18267134	ECC-1	luminal epithelium:	n/a	chr17:18266498-18266514 chr17:18266949-18266965 chr17:18266562-18266578
25	POLR2A	chr17:18266595-18267174	HepG2	liver:	n/a	n/a
26	POLR2A	chr17:18266505-18267247	GM12891	blood:	n/a	n/a
27	SP4	chr17:18266623-18267119	H1-hESC	embryonic stem cell:	n/a	chr17:18266865-18266876 chr17:18266863-18266879
28	SP1	chr17:18266581-18267155	GM12878	blood:	n/a	chr17:18266866-18266875 chr17:18266975-18266984 chr17:18266881-18266902 chr17:18266866-18266876 chr17:18266865-18266877 chr17:18266865-18266876 chr17:18266867-18266876 chr17:18266865-18266877 chr17:18266866-18266875 chr17:18266866-18266876 chr17:18267013-18267022
29	FOS	chr17:18266681-18267102	K562	blood:	n/a	n/a
30	POLR2A	chr17:18266369-18267222	PFSK-1	brain:	n/a	n/a
31	RAD21	chr17:18266070-18267064	H1-hESC	embryonic stem cell:	n/a	chr17:18266949-18266962 chr17:18266759-18266772
32	USF1	chr17:18266304-18267225	HCT-116	colon:	n/a	chr17:18266498-18266514 chr17:18266949-18266965 chr17:18266562-18266578
33	REST	chr17:18266647-18267001	PFSK-1	brain:	n/a	chr17:18266748-18266761
34	UBTF	chr17:18266391-18267165	K562	blood:	n/a	n/a
35	POLR2A	chr17:18266547-18267107	A549	lung:	n/a	n/a
36	RFX5	chr17:18265868-18267207	Hela-S3	cervix:	n/a	n/a
37	HA-E2F1	chr17:18266371-18267165	Hela-S3	cervix:	n/a	chr17:18266707-18266717 chr17:18266867-18266876
38	USF2	chr17:18266212-18267212	Hela-S3	cervix:	n/a	chr17:18266770-18266781 chr17:18266498-18266514 chr17:18266949-18266965 chr17:18266562-18266578
39	USF1	chr17:18266538-18267037	H1-hESC	embryonic stem cell:	n/a	chr17:18266949-18266965 chr17:18266562-18266578
40	POLR2A	chr17:18266517-18267189	HepG2	liver:	n/a	n/a
41	CHD2	chr17:18266662-18267055	HepG2	liver:	n/a	chr17:18266975-18266985
42	POLR2A	chr17:18266463-18267213	HCT-116	colon:	n/a	n/a
43	MAX	chr17:18266280-18267145	K562	blood:	n/a	chr17:18266762-18266778 chr17:18266770-18266781 chr17:18266771-18266780 chr17:18266771-18266780
44	JUND	chr17:18266422-18267182	K562	blood:	n/a	n/a
45	TCF12	chr17:18265811-18267244	A549	lung:	n/a	n/a
46	POLR2A	chr17:18266371-18267205	ECC-1	luminal epithelium:	n/a	n/a
47	MYC	chr17:18266257-18267199	NB4	blood:	n/a	chr17:18266762-18266778 chr17:18266770-18266781 chr17:18266771-18266780 chr17:18266771-18266780
48	ETS1	chr17:18266582-18267053	A549	lung:	n/a	chr17:18266706-18266717 chr17:18266867-18266878
49	NRF1	chr17:18266535-18267192	H1-hESC	embryonic stem cell:	n/a	chr17:18266998-18267009 chr17:18266867-18266876 chr17:18266954-18266963
50	PAX5	chr17:18266530-18267160	GM12878	blood:	n/a	chr17:18266894-18266912

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

Variant related genes	Relation type
SHMT1	TF binding region
ENSG00000176994	Chromatin interaction
ENSG00000177302	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12950117	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1563632	0.80[ASN][1000 genomes]
rs1682280	0.81[EUR][1000 genomes]
rs2688030	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2688036	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2688052	0.80[EUR][1000 genomes]
rs28597812	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4398149	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4925179	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs593297	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs638318	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs641028	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs651234	0.91[ASN][1000 genomes]
rs652093	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs669340	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8080936	0.83[EUR][1000 genomes]
rs921985	0.81[ASN][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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs638416	SHMT1	cis	Muscle Skeletal	GTEx
rs638416	USP32P2	cis	Thyroid	GTEx
rs638416	USP32P2	cis	Artery Tibial	GTEx
rs638416	LGALS9C	cis	Whole Blood	GTEx
rs638416	SHMT1	cis	Artery Aorta	GTEx
rs638416	FAM106A	cis	lung	GTEx
rs638416	FAM106A	cis	Thyroid	GTEx
rs638416	SHMT1	cis	Artery Tibial	GTEx
rs638416	USP32P2	cis	lung	GTEx
rs638416	SHMT1	cis	multi-tissue	Pritchard
rs638416	SHMT1	cis	Nerve Tibial	GTEx
rs638416	SHMT1	cis	Whole Blood	GTEx
rs638416	USP32P2	cis	Nerve Tibial	GTEx
rs638416	USP32P2	cis	Whole Blood	GTEx
rs638416	USP32P2	cis	Esophagus Mucosa	GTEx
rs638416	SHMT1	cis	Esophagus Muscularis	GTEx
rs638416	SHMT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18265200-18267000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr17:18265200-18267000	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr17:18265200-18267200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr17:18265200-18267200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr17:18265200-18267400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:18265400-18267000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr17:18265400-18267000	Active TSS	Fetal Kidney	kidney
8	chr17:18265400-18267200	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr17:18265400-18267200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr17:18265400-18267400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr17:18265600-18267000	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr17:18265600-18267000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr17:18265600-18267000	Active TSS	Brain Cingulate Gyrus	brain
14	chr17:18265600-18267000	Active TSS	HMEC	breast
15	chr17:18265600-18267200	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr17:18265600-18267200	Active TSS	A549	lung
17	chr17:18265800-18267000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr17:18265800-18267000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr17:18265800-18267000	Active TSS	Esophagus	oesophagus
20	chr17:18265800-18267000	Active TSS	Rectal Smooth Muscle	rectum
21	chr17:18265800-18267200	Active TSS	H9 Cell Line	embryonic stem cell
22	chr17:18265800-18267200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr17:18265800-18267200	Active TSS	Brain Substantia Nigra	brain
24	chr17:18265800-18267200	Active TSS	NHDF-Ad	bronchial
25	chr17:18265800-18267400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr17:18265800-18267400	Active TSS	Hela-S3	cervix
27	chr17:18265800-18267600	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr17:18266000-18267000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr17:18266000-18267200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:18266000-18267200	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr17:18266000-18267200	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr17:18266000-18267200	Active TSS	Brain Anterior Caudate	brain
33	chr17:18266000-18267200	Active TSS	Fetal Lung	lung
34	chr17:18266000-18267200	Active TSS	Gastric	stomach
35	chr17:18266000-18267200	Active TSS	Lung	lung
36	chr17:18266000-18267200	Active TSS	Right Atrium	heart
37	chr17:18266000-18267200	Active TSS	Right Ventricle	heart
38	chr17:18266000-18267200	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr17:18266000-18267200	Active TSS	HSMM	muscle
40	chr17:18266000-18267200	Active TSS	HSMMtube	muscle
41	chr17:18266000-18267400	Active TSS	K562	blood
42	chr17:18266200-18267000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr17:18266200-18267000	Active TSS	Primary T cells from cord blood	blood
44	chr17:18266200-18267000	Active TSS	Colonic Mucosa	Colon
45	chr17:18266200-18267000	Active TSS	Fetal Intestine Small	intestine
46	chr17:18266200-18267000	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr17:18266200-18267000	Active TSS	GM12878-XiMat	blood
48	chr17:18266200-18267200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:18266200-18267200	Active TSS	Brain Angular Gyrus	brain
50	chr17:18266200-18267200	Active TSS	Fetal Heart	heart

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