Variant report

Variant	rs257630
Chromosome Location	chr16:58755176-58755177
allele	C/T
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	TEAD4	chr16:58754670-58755453	HepG2	liver:	n/a	n/a
2	ARID3A	chr16:58754790-58755439	HepG2	liver:	n/a	n/a
3	REST	chr16:58754842-58755271	HepG2	liver:	n/a	n/a
4	FOXA1	chr16:58754801-58755207	T-47D	breast:	n/a	n/a
5	FOXA1	chr16:58754649-58755493	HepG2	liver:	n/a	n/a
6	CHD2	chr16:58754943-58755402	HepG2	liver:	n/a	n/a
7	MAFF	chr16:58754922-58755285	HepG2	liver:	n/a	n/a
8	MBD4	chr16:58754666-58755485	HepG2	liver:	n/a	n/a
9	ZBTB33	chr16:58754774-58755235	HepG2	liver:	n/a	n/a
10	MXI1	chr16:58754858-58755487	HepG2	liver:	n/a	n/a
11	FOXA1	chr16:58754665-58755523	HepG2	liver:	n/a	n/a
12	FOXA2	chr16:58754761-58755517	HepG2	liver:	n/a	n/a
13	CTCF	chr16:58755160-58755310	HepG2	liver:	n/a	n/a
14	HNF4A	chr16:58754810-58755425	HepG2	liver:	n/a	chr16:58755092-58755114 chr16:58755350-58755358
15	TCF7L2	chr16:58754865-58755279	HepG2	liver:	n/a	n/a
16	RXRA	chr16:58754746-58755383	HepG2	liver:	n/a	n/a
17	BHLHE40	chr16:58754909-58755434	HepG2	liver:	n/a	n/a
18	SP1	chr16:58754757-58755484	HepG2	liver:	n/a	n/a
19	EP300	chr16:58754816-58755543	HepG2	liver:	n/a	n/a
20	FOXA1	chr16:58754626-58755476	HepG2	liver:	n/a	n/a
21	FOXA2	chr16:58753912-58755672	HepG2	liver:	n/a	chr16:58754274-58754286
22	EP300	chr16:58754769-58755480	HepG2	liver:	n/a	n/a
23	MAFK	chr16:58754921-58755256	HepG2	liver:	n/a	chr16:58755113-58755124 chr16:58755111-58755125
24	NR2F2	chr16:58754554-58755571	HepG2	liver:	n/a	n/a
25	EP300	chr16:58754727-58755530	HepG2	liver:	n/a	n/a
26	NFIC	chr16:58754771-58755354	HepG2	liver:	n/a	n/a
27	MAX	chr16:58754912-58755395	HepG2	liver:	n/a	chr16:58755243-58755259
28	HDAC2	chr16:58754815-58755282	HepG2	liver:	n/a	n/a
29	SMC3	chr16:58754920-58755372	HepG2	liver:	n/a	chr16:58755293-58755307
30	RCOR1	chr16:58754877-58755295	HepG2	liver:	n/a	n/a
31	MYBL2	chr16:58754650-58755562	HepG2	liver:	n/a	n/a
32	REST	chr16:58754880-58755193	HepG2	liver:	n/a	n/a
33	MAFK	chr16:58754856-58755462	HepG2	liver:	n/a	chr16:58755113-58755124 chr16:58755111-58755125
34	CEBPB	chr16:58754867-58755384	HepG2	liver:	n/a	n/a
35	MAX	chr16:58754744-58755644	HepG2	liver:	n/a	chr16:58755243-58755259
36	MBD4	chr16:58754834-58755594	HepG2	liver:	n/a	n/a
37	HDAC2	chr16:58754718-58755359	HepG2	liver:	n/a	n/a
38	FOXA1	chr16:58754816-58755223	T-47D	breast:	n/a	n/a
39	RAD21	chr16:58754977-58755499	HepG2	liver:	n/a	chr16:58755295-58755308 chr16:58755297-58755309
40	NFIC	chr16:58754760-58755455	HepG2	liver:	n/a	n/a
41	MAZ	chr16:58754883-58755468	HepG2	liver:	n/a	chr16:58755243-58755259
42	FOXA1	chr16:58754667-58755561	HepG2	liver:	n/a	n/a
43	NR2F2	chr16:58754878-58755247	MCF-7	breast:	n/a	n/a
44	HNF4G	chr16:58754822-58755262	HepG2	liver:	n/a	chr16:58755092-58755114
45	HNF4A	chr16:58754824-58755274	HepG2	liver:	n/a	chr16:58755092-58755114
46	NR2F2	chr16:58754719-58755591	HepG2	liver:	n/a	n/a
47	CEBPB	chr16:58754888-58755221	HepG2	liver:	n/a	n/a
48	MYBL2	chr16:58754704-58755498	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:58754816..58757724-chr16:58758002..58760013,2	K562	blood:
2	chr16:58751934..58754390-chr16:58755126..58757009,2	K562	blood:
3	chr16:58754800..58755486-chr16:58767790..58768509,2	MCF-7	breast:

Variant related genes	Relation type
GOT2	TF binding region
ENSG00000245768	Chromatin interaction
ENSG00000125166	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1058192	0.88[EUR][1000 genomes]
rs11076262	0.96[CEU][hapmap];0.97[TSI][hapmap]
rs14221	0.92[EUR][1000 genomes]
rs1436429	0.80[EUR][1000 genomes]
rs1595181	0.96[CEU][hapmap];0.97[TSI][hapmap]
rs1615326	0.83[CHD][hapmap]
rs1646267	0.90[EUR][1000 genomes]
rs171786	0.96[CEU][hapmap];0.90[GIH][hapmap];0.92[EUR][1000 genomes]
rs173992	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs183757	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs185397	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs187277	0.92[EUR][1000 genomes]
rs190473	0.88[EUR][1000 genomes]
rs257616	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs257617	0.92[EUR][1000 genomes]
rs257618	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[EUR][1000 genomes]
rs257619	0.92[EUR][1000 genomes]
rs257620	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap]
rs257621	0.92[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs257631	0.92[EUR][1000 genomes]
rs257632	0.92[EUR][1000 genomes]
rs257633	0.92[EUR][1000 genomes]
rs257634	0.90[EUR][1000 genomes]
rs257636	0.88[EUR][1000 genomes]
rs257637	0.92[EUR][1000 genomes]
rs257638	0.89[EUR][1000 genomes]
rs863944	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][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	esv2758427	chr16:58579005-58876037	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2758650	chr16:58579005-58876037	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS 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 lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv510686	chr16:58646119-58765894	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv1065296	chr16:58738198-58837859	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	n/a
5	nsv1065269	chr16:58743487-58972224	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs257630	GOT2	cis	parietal	SCAN
rs257630	GOT2	cis	cerebellum	SCAN
rs257630	CETP	cis	parietal	SCAN
rs257630	GOT2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:58738200-58757800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr16:58738200-58758000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:58738400-58759800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr16:58738400-58766600	Weak transcription	Stomach Mucosa	stomach
5	chr16:58739000-58757800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr16:58739200-58758000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr16:58739200-58758000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr16:58739200-58758400	Strong transcription	Primary T cells from cord blood	blood
9	chr16:58739200-58759000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr16:58739200-58759600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr16:58739400-58758400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr16:58739600-58757600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr16:58739600-58757800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr16:58739600-58758000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr16:58739600-58758200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr16:58739600-58758400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr16:58739800-58757800	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr16:58739800-58757800	Strong transcription	Duodenum Mucosa	Duodenum
19	chr16:58739800-58757800	Strong transcription	Thymus	Thymus
20	chr16:58739800-58759200	Strong transcription	Dnd41	blood
21	chr16:58739800-58759800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr16:58740000-58755200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr16:58740400-58756400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr16:58740400-58757800	Strong transcription	Fetal Intestine Large	intestine
25	chr16:58740400-58757800	Strong transcription	Ovary	ovary
26	chr16:58740400-58757800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr16:58740400-58758000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr16:58740400-58759000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr16:58740600-58757800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr16:58743000-58757800	Strong transcription	HUVEC	blood vessel
31	chr16:58743400-58759000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr16:58744800-58757800	Strong transcription	Fetal Brain Female	brain
33	chr16:58745000-58757800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr16:58745000-58757800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr16:58745000-58757800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr16:58745000-58758400	Strong transcription	Left Ventricle	heart
37	chr16:58745200-58757600	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr16:58745200-58758400	Strong transcription	Osteobl	bone
39	chr16:58745400-58758000	Strong transcription	Fetal Intestine Small	intestine
40	chr16:58745600-58757800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr16:58747200-58757600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr16:58747600-58757800	Strong transcription	Fetal Muscle Leg	muscle
43	chr16:58747800-58767000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr16:58748000-58756600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr16:58748000-58757200	Strong transcription	Brain Germinal Matrix	brain
46	chr16:58748800-58755800	Strong transcription	Brain Cingulate Gyrus	brain
47	chr16:58748800-58757200	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr16:58748800-58757600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr16:58748800-58757600	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr16:58748800-58757600	Strong transcription	A549	lung

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