Variant report

Variant	rs4600490
Chromosome Location	chr16:74598125-74598126
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr16:74597645-74598137	A549	lung:	n/a	n/a
2	CBX3	chr16:74597609-74598260	HCT-116	colon:	n/a	n/a
3	MAFK	chr16:74597636-74598860	K562	blood:	n/a	chr16:74597809-74597824
4	MYC	chr16:74597706-74598163	K562	blood:	n/a	n/a
5	JUN	chr16:74597481-74598320	K562	blood:	n/a	n/a
6	BCLAF1	chr16:74597595-74598143	K562	blood:	n/a	n/a
7	MAX	chr16:74597642-74598170	NB4	blood:	n/a	n/a
8	CEBPB	chr16:74597533-74598244	K562	blood:	n/a	n/a
9	CEBPD	chr16:74597572-74598172	K562	blood:	n/a	n/a
10	MAX	chr16:74597764-74598193	K562	blood:	n/a	n/a
11	FOSL1	chr16:74597551-74598291	HCT-116	colon:	n/a	chr16:74597887-74597898
12	CCNT2	chr16:74597709-74598152	K562	blood:	n/a	n/a
13	CEBPB	chr16:74597620-74598229	HCT-116	colon:	n/a	n/a
14	TBP	chr16:74598024-74598129	K562	blood:	n/a	n/a
15	E2F6	chr16:74597763-74598183	K562	blood:	n/a	n/a
16	NR2F2	chr16:74597522-74598167	K562	blood:	n/a	n/a
17	TRIM28	chr16:74597590-74598173	K562	blood:	n/a	n/a
18	CUX1	chr16:74597733-74598169	K562	blood:	n/a	n/a
19	MAX	chr16:74597595-74598432	HCT-116	colon:	n/a	n/a
20	TBL1XR1	chr16:74597716-74598449	K562	blood:	n/a	n/a
21	ATF3	chr16:74597583-74598129	K562	blood:	n/a	n/a
22	JUND	chr16:74597623-74598274	HCT-116	colon:	n/a	chr16:74597887-74597898
23	MAX	chr16:74597729-74598167	K562	blood:	n/a	n/a
24	JUND	chr16:74597545-74598222	HCT-116	colon:	n/a	chr16:74597887-74597898
25	FOSL1	chr16:74597612-74598221	HCT-116	colon:	n/a	chr16:74597887-74597898
26	MYC	chr16:74597621-74598174	NB4	blood:	n/a	n/a
27	BHLHE40	chr16:74597758-74598195	K562	blood:	n/a	n/a
28	ZC3H11A	chr16:74597955-74598195	K562	blood:	n/a	n/a
29	SP1	chr16:74597669-74598357	HCT-116	colon:	n/a	n/a
30	CBX3	chr16:74597584-74598246	K562	blood:	n/a	n/a
31	TEAD4	chr16:74597566-74598273	K562	blood:	n/a	n/a
32	MYC	chr16:74597664-74598242	K562	blood:	n/a	n/a
33	MAX	chr16:74597719-74598280	K562	blood:	n/a	n/a
34	MAX	chr16:74597672-74598327	HCT-116	colon:	n/a	n/a
35	MYC	chr16:74597688-74598314	K562	blood:	n/a	n/a
36	JUN	chr16:74597692-74598139	K562	blood:	n/a	n/a
37	JUND	chr16:74597639-74598154	K562	blood:	n/a	chr16:74597887-74597898
38	MYC	chr16:74597650-74598349	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:74597481..74599946-chr16:74698831..74700953,2	MCF-7	breast:
2	chr16:74596282..74598588-chr16:74639411..74642342,2	K562	blood:

No data

Variant related genes	Relation type
GLG1	TF binding region
ENSG00000168411	Chromatin interaction
ENSG00000090863	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1019572	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs1019573	0.84[JPT][hapmap]
rs10468356	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10500587	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs11149722	0.82[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap]
rs11639812	0.82[CHB][hapmap];0.80[CHD][hapmap];0.84[JPT][hapmap]
rs11644298	0.82[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs11648868	0.95[CHD][hapmap];0.84[JPT][hapmap]
rs12325017	0.82[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs12445991	0.82[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs12446054	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs12448026	0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs12598701	1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap]
rs13339161	1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.88[LWK][hapmap];0.95[YRI][hapmap]
rs13359	0.82[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap]
rs1469140	0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.85[LWK][hapmap];0.95[YRI][hapmap]
rs2098754	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs2288053	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs2303275	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs2303278	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2303281	0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.95[YRI][hapmap]
rs2550824	0.86[ASN][1000 genomes]
rs3785312	0.84[JPT][hapmap]
rs3826239	0.84[JPT][hapmap]
rs3923201	0.93[ASN][1000 genomes]
rs4072222	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs4072450	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs4243108	1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap]
rs4438331	0.82[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap]
rs4887772	1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap];0.88[LWK][hapmap];0.95[YRI][hapmap]
rs4887776	1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap]
rs4887777	0.92[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap]
rs4887779	1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs4888238	0.82[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.82[LWK][hapmap];0.82[YRI][hapmap]
rs4888240	0.80[CHD][hapmap]
rs4888242	0.82[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap]
rs4888253	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.89[LWK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4888255	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4888256	0.91[CHB][hapmap];0.90[CHD][hapmap];0.84[JPT][hapmap]
rs4888266	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs55960814	0.87[ASN][1000 genomes]
rs62054177	0.87[ASN][1000 genomes]
rs6564117	0.92[CHB][hapmap];0.80[CHD][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap]
rs6564141	0.90[ASN][1000 genomes]
rs6564142	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6564145	0.81[ASN][1000 genomes]
rs6564147	0.80[ASN][1000 genomes]
rs6564152	0.80[ASN][1000 genomes]
rs6564153	0.80[ASN][1000 genomes]
rs6564154	0.91[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap]
rs6564157	0.82[CHB][hapmap]
rs67414268	0.85[ASN][1000 genomes]
rs71392603	0.94[ASN][1000 genomes]
rs7185026	0.91[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs7185722	0.80[ASN][1000 genomes]
rs7189123	1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.88[LWK][hapmap];0.91[YRI][hapmap]
rs7193959	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs7194143	0.82[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap]
rs7201105	0.84[ASN][1000 genomes]
rs7203452	0.91[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs7204382	0.90[CHB][hapmap];0.80[CHD][hapmap]
rs7204804	0.91[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs7205258	1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs7205813	0.93[ASN][1000 genomes]
rs7342732	1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap]
rs7359390	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8045848	0.82[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap]
rs8046158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8048239	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs8049138	0.91[ASN][1000 genomes]
rs8050624	1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap]
rs8050668	0.93[ASN][1000 genomes]
rs8050850	0.95[ASN][1000 genomes]
rs8051990	0.93[ASN][1000 genomes]
rs8052389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8052923	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs8053369	0.93[ASN][1000 genomes]
rs8055380	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8055784	0.91[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap]
rs8055803	0.80[ASN][1000 genomes]
rs8056718	0.83[ASN][1000 genomes]
rs8058256	0.83[ASN][1000 genomes]
rs8058437	0.80[ASN][1000 genomes]
rs8058692	0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs8058922	0.91[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap]
rs8062404	0.83[ASN][1000 genomes]
rs918782	0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]
rs9888950	0.92[ASN][1000 genomes]
rs9888968	0.87[ASN][1000 genomes]
rs9888976	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.86[ASN][1000 genomes]
rs9923616	1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap]
rs9923644	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9927073	0.91[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap]
rs9929483	0.91[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap]
rs9929933	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9930003	0.95[ASN][1000 genomes]
rs9931225	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs9932831	0.81[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap]
rs9938833	0.91[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap]
rs9938859	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948443	chr16:73994997-74627711	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
3	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv1060629	chr16:74483574-74660669	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv1062517	chr16:74483574-74710623	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv833279	chr16:74490746-74663073	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
8	nsv906905	chr16:74527618-74679244	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4600490	RFWD3	cis	multi-tissue	Pritchard
rs4600490	GLG1	cis	parietal	SCAN
rs4600490	MLKL	cis	multi-tissue	Pritchard

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74537600-74604800	Weak transcription	Thymus	Thymus
2	chr16:74563200-74622400	Weak transcription	Fetal Stomach	stomach
3	chr16:74583000-74617200	Weak transcription	Fetal Muscle Leg	muscle
4	chr16:74585400-74601000	Weak transcription	Fetal Thymus	thymus
5	chr16:74587600-74612200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr16:74588200-74623200	Weak transcription	Primary B cells from cord blood	blood
7	chr16:74589800-74626800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr16:74590000-74607000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr16:74590200-74614600	Weak transcription	Adipose Nuclei	Adipose
10	chr16:74590400-74607600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr16:74590600-74601200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr16:74591000-74602600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr16:74591000-74602600	Weak transcription	NHEK	skin
14	chr16:74591000-74624000	Weak transcription	Aorta	Aorta
15	chr16:74591800-74602800	Weak transcription	Stomach Mucosa	stomach
16	chr16:74591800-74613600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr16:74593000-74602800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr16:74593200-74608600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr16:74593800-74607200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr16:74595000-74598200	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr16:74595000-74622600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr16:74595200-74601800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr16:74595200-74607000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr16:74595200-74607400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr16:74595400-74601800	Weak transcription	Fetal Brain Female	brain
26	chr16:74595600-74598200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr16:74595600-74600200	Enhancers	Psoas Muscle	Psoas
28	chr16:74595800-74601000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr16:74595800-74603000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr16:74595800-74604600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr16:74595800-74605000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr16:74595800-74608400	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr16:74596000-74598600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr16:74596000-74599000	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr16:74596000-74604400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr16:74596000-74604600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr16:74596000-74614400	Weak transcription	Colon Smooth Muscle	Colon
38	chr16:74596200-74601000	Weak transcription	Brain Angular Gyrus	brain
39	chr16:74596200-74602800	Weak transcription	Small Intestine	intestine
40	chr16:74596200-74602800	Weak transcription	Hela-S3	cervix
41	chr16:74596200-74607200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr16:74596200-74609400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr16:74596400-74598200	Enhancers	Left Ventricle	heart
44	chr16:74596400-74607800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr16:74596800-74598200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr16:74596800-74598600	Enhancers	Fetal Intestine Large	intestine
47	chr16:74596800-74599400	Weak transcription	Fetal Heart	heart
48	chr16:74597000-74599400	Enhancers	Primary T cells fromperipheralblood	blood
49	chr16:74597000-74599400	Enhancers	K562	blood
50	chr16:74597000-74599600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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