Variant report

Variant	rs3783638
Chromosome Location	chr14:55348373-55348374
allele	A/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	CTCF	chr14:55348260-55348410	AG10803	skin:	n/a	n/a
2	RFX5	chr14:55348044-55349924	SK-N-SH	brain:	n/a	chr14:55349620-55349629 chr14:55349597-55349605
3	TAF1	chr14:55347970-55348442	GM12878	blood:	n/a	n/a
4	BATF	chr14:55347981-55348418	GM12878	blood:	n/a	n/a
5	CTCF	chr14:55348320-55348470	GM12873	blood:	n/a	n/a
6	CTCF	chr14:55348240-55348390	NHDF-neo	bronchial:	n/a	n/a
7	MYC	chr14:55348160-55348592	MCF10A-Er-Src	breast:	n/a	n/a
8	CTCF	chr14:55348260-55348410	BJ	skin:	n/a	n/a
9	POLR2A	chr14:55348066-55348528	GM12892	blood:	n/a	n/a
10	PML	chr14:55347841-55348972	GM12878	blood:	n/a	n/a
11	CTCF	chr14:55348300-55348450	AG09309	skin:	n/a	n/a
12	CTCF	chr14:55348329-55348424	ProgFib	skin:	n/a	n/a
13	FOXM1	chr14:55347932-55348410	GM12878	blood:	n/a	n/a
14	CTCF	chr14:55348336-55348382	Kidney_OC	kidney:	n/a	n/a
15	POLR2A	chr14:55348056-55348862	HUVEC	blood vessel:	n/a	n/a
16	WRNIP1	chr14:55348003-55348489	GM12878	blood:	n/a	n/a
17	POLR2A	chr14:55348242-55348451	GM12878	blood:	n/a	n/a
18	YY1	chr14:55348224-55348411	K562	blood:	n/a	chr14:55348322-55348332
19	BCLAF1	chr14:55347924-55348724	GM12878	blood:	n/a	chr14:55348195-55348204
20	BATF	chr14:55347926-55348447	GM12878	blood:	n/a	n/a
21	TBP	chr14:55347985-55349003	GM12878	blood:	n/a	n/a
22	MTA3	chr14:55347981-55348942	GM12878	blood:	n/a	n/a
23	MTA3	chr14:55347857-55348866	GM12878	blood:	n/a	n/a
24	YY1	chr14:55348179-55348424	GM12892	blood:	n/a	chr14:55348322-55348332
25	ATF2	chr14:55348036-55348807	GM12878	blood:	n/a	n/a
26	POLR2A	chr14:55347929-55349095	GM12878	blood:	n/a	n/a
27	CTCF	chr14:55348320-55348470	HPAF	blood vessel:	n/a	n/a
28	CTCF	chr14:55348240-55348390	GM06990	blood:	n/a	n/a
29	CTCF	chr14:55348320-55348470	BE2_C	brain:	n/a	n/a
30	STAT1	chr14:55348236-55348490	GM12878	blood:	n/a	n/a
31	YY1	chr14:55348152-55348458	GM12878	blood:	n/a	chr14:55348322-55348332
32	E2F4	chr14:55348220-55348483	MCF10A-Er-Src	breast:	n/a	n/a
33	RUNX3	chr14:55348008-55348483	GM12878	blood:	n/a	n/a
34	CTCF	chr14:55348280-55348430	HCPEpiC	choroid plexus:	n/a	n/a
35	CTCF	chr14:55348300-55348450	BJ	skin:	n/a	n/a
36	CTCF	chr14:55348300-55348450	AG09319	gingival:	n/a	n/a
37	JUND	chr14:55347787-55348426	GM12878	blood:	n/a	chr14:55348201-55348213
38	EBF1	chr14:55348030-55348781	GM12878	blood:	n/a	n/a
39	BCLAF1	chr14:55347970-55348963	GM12878	blood:	n/a	chr14:55348195-55348204 chr14:55348801-55348810
40	CTCF	chr14:55348260-55348410	HPAF	blood vessel:	n/a	n/a
41	POLR2A	chr14:55347917-55348408	GM12878	blood:	n/a	n/a
42	TCF7L2	chr14:55348298-55348497	PANC-1	pancreas:	n/a	n/a
43	CTCF	chr14:55348320-55348470	AG09319	gingival:	n/a	n/a
44	POLR2A	chr14:55348208-55348686	U87	brain:	n/a	n/a
45	YY1	chr14:55348150-55348477	SK-N-SH_RA	brain:	n/a	chr14:55348322-55348332
46	CTCF	chr14:55348240-55348390	HCFaa	heart:	n/a	n/a
47	NFIC	chr14:55347944-55348464	GM12878	blood:	n/a	n/a
48	POLR2A	chr14:55348315-55348426	HUVEC	blood vessel:	n/a	n/a
49	EP300	chr14:55347996-55348597	GM12878	blood:	n/a	chr14:55348166-55348180
50	MXI1	chr14:55347981-55348944	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55348331..55350043-chr14:55361093..55363707,2	K562	blood:

Variant related genes	Relation type
MIR4308	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10133449	0.82[AFR][1000 genomes]
rs10139282	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10498471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12147422	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17128050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap]
rs2183080	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs28477407	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs28542181	0.81[AFR][1000 genomes]
rs28757745	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3783637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61702394	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs66989494	0.83[EUR][1000 genomes]
rs7492600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs8003903	0.92[EUR][1000 genomes]
rs8004018	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8004445	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010282	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs8010461	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530042	chr14:55208170-55386966	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv932970	chr14:55326559-55532749	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv3323442	chr14:55346027-55348775	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
4	esv3358447	chr14:55346377-55348700	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	esv3322576	chr14:55346802-55348400	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3783638	L2HGDH	cis	parietal	SCAN
rs3783638	GCH1	cis	parietal	SCAN
rs3783638	KTN1	cis	cerebellum	SCAN
rs3783638	GCH1	cis	cerebellum	SCAN
rs3783638	WDHD1	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55337600-55348600	Weak transcription	Hela-S3	cervix
2	chr14:55345400-55354800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr14:55345400-55368200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr14:55347600-55348400	Flanking Active TSS	Liver	Liver
5	chr14:55347600-55349000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr14:55347600-55349200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr14:55347600-55349400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr14:55347600-55349400	Flanking Active TSS	Dnd41	blood
9	chr14:55347800-55348400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr14:55347800-55348400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr14:55347800-55348400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
12	chr14:55347800-55348400	Active TSS	GM12878-XiMat	blood
13	chr14:55347800-55348600	Active TSS	Muscle Satellite Cultured Cells	--
14	chr14:55347800-55348600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr14:55347800-55348600	Active TSS	Monocytes-CD14+_RO01746	blood
16	chr14:55347800-55348800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr14:55347800-55348800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr14:55347800-55348800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr14:55347800-55348800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr14:55347800-55348800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr14:55347800-55348800	Active TSS	Right Atrium	heart
22	chr14:55347800-55348800	Active TSS	NHDF-Ad	bronchial
23	chr14:55347800-55348800	Active TSS	NHLF	lung
24	chr14:55347800-55349000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr14:55347800-55349000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr14:55347800-55349000	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr14:55347800-55349000	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr14:55347800-55349000	Active TSS	Aorta	Aorta
29	chr14:55347800-55349000	Active TSS	Psoas Muscle	Psoas
30	chr14:55347800-55349000	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr14:55347800-55349000	Active TSS	Thymus	Thymus
32	chr14:55347800-55349000	Flanking Active TSS	HMEC	breast
33	chr14:55347800-55349200	Active TSS	Rectal Smooth Muscle	rectum
34	chr14:55347800-55349200	Flanking Active TSS	NHEK	skin
35	chr14:55347800-55349600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr14:55348000-55348400	Active TSS	Primary hematopoietic stem cells	blood
37	chr14:55348000-55348400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
38	chr14:55348000-55348400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr14:55348000-55348400	Active TSS	Colonic Mucosa	Colon
40	chr14:55348000-55348400	Active TSS	Placenta	Placenta
41	chr14:55348000-55348400	Active TSS	Lung	lung
42	chr14:55348000-55348400	Flanking Active TSS	HSMMtube	muscle
43	chr14:55348000-55348400	Active TSS	HUVEC	blood vessel
44	chr14:55348000-55348400	Active TSS	NH-A	brain
45	chr14:55348000-55348600	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr14:55348000-55348600	Active TSS	Esophagus	oesophagus
47	chr14:55348000-55348600	Active TSS	HSMM	muscle
48	chr14:55348000-55348800	Active TSS	Primary T cells fromperipheralblood	blood
49	chr14:55348000-55348800	Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr14:55348000-55348800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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