Variant report

Variant	rs6499335
Chromosome Location	chr16:70780092-70780093
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	POLR2A	chr16:70779897-70781047	HepG2	liver:	n/a	n/a
2	FOXA1	chr16:70779722-70780245	HepG2	liver:	n/a	chr16:70779963-70779975
3	BHLHE40	chr16:70779983-70780216	HepG2	liver:	n/a	n/a
4	MYC	chr16:70779954-70781124	K562	blood:	n/a	chr16:70780147-70780154 chr16:70780788-70780797 chr16:70780789-70780798 chr16:70780144-70780155 chr16:70780406-70780416 chr16:70780145-70780154 chr16:70780120-70780130
5	MYC	chr16:70780074-70780870	MCF-7	breast:	n/a	chr16:70780147-70780154 chr16:70780788-70780797 chr16:70780789-70780798 chr16:70780144-70780155 chr16:70780406-70780416 chr16:70780145-70780154 chr16:70780120-70780130
6	NFIC	chr16:70779803-70781151	SK-N-SH	brain:	n/a	n/a
7	JUND	chr16:70779962-70781274	HepG2	liver:	n/a	chr16:70780787-70780798 chr16:70780350-70780359 chr16:70780787-70780799 chr16:70780788-70780797 chr16:70780789-70780798 chr16:70780789-70780797 chr16:70780789-70780796 chr16:70780349-70780358
8	EGR1	chr16:70779886-70780266	K562	blood:	n/a	chr16:70780120-70780133 chr16:70780120-70780133 chr16:70780119-70780134
9	MYC	chr16:70779995-70781206	K562	blood:	n/a	chr16:70780147-70780154 chr16:70780788-70780797 chr16:70780789-70780798 chr16:70780144-70780155 chr16:70780406-70780416 chr16:70780145-70780154 chr16:70780120-70780130
10	FOXA2	chr16:70779746-70781154	A549	lung:	n/a	chr16:70779963-70779975
11	MAX	chr16:70779884-70781330	MCF-7	breast:	n/a	chr16:70780147-70780154 chr16:70780788-70780797 chr16:70780789-70780798 chr16:70780144-70780155 chr16:70780406-70780416 chr16:70780145-70780154 chr16:70780120-70780130
12	USF1	chr16:70779932-70780361	A549	lung:	n/a	n/a
13	MYC	chr16:70779901-70781267	MCF10A-Er-Src	breast:	n/a	chr16:70780147-70780154 chr16:70780788-70780797 chr16:70780789-70780798 chr16:70780144-70780155 chr16:70780406-70780416 chr16:70780145-70780154 chr16:70780120-70780130
14	MXI1	chr16:70779989-70781277	HepG2	liver:	n/a	chr16:70780407-70780416
15	USF1	chr16:70779995-70780375	ECC-1	luminal epithelium:	n/a	n/a
16	YY1	chr16:70780003-70780964	A549	lung:	n/a	n/a
17	STAT3	chr16:70779933-70780303	MCF10A-Er-Src	breast:	n/a	chr16:70780110-70780122
18	POLR2A	chr16:70779946-70780331	HepG2	liver:	n/a	n/a
19	JUND	chr16:70780032-70781307	HepG2	liver:	n/a	chr16:70780787-70780798 chr16:70780350-70780359 chr16:70780787-70780799 chr16:70780788-70780797 chr16:70780789-70780798 chr16:70780789-70780797 chr16:70780789-70780796 chr16:70780349-70780358
20	USF1	chr16:70779903-70780411	ECC-1	luminal epithelium:	n/a	n/a
21	EGR1	chr16:70779783-70780402	MCF-7	breast:	n/a	chr16:70780120-70780133 chr16:70780120-70780133 chr16:70780119-70780134
22	SIX5	chr16:70780056-70781156	A549	lung:	n/a	n/a
23	POLR2A	chr16:70779816-70781048	U87	brain:	n/a	n/a
24	MYBL2	chr16:70779746-70781481	HepG2	liver:	n/a	n/a
25	MBD4	chr16:70779693-70781374	HepG2	liver:	n/a	n/a
26	POLR2A	chr16:70779928-70781330	HepG2	liver:	n/a	n/a
27	EP300	chr16:70779896-70781267	HepG2	liver:	n/a	chr16:70780789-70780798 chr16:70780788-70780797 chr16:70780011-70780021
28	MAZ	chr16:70779623-70781476	IMR90	lung:	n/a	chr16:70780147-70780154 chr16:70780788-70780797 chr16:70780789-70780798 chr16:70780144-70780155 chr16:70780406-70780416 chr16:70780145-70780154 chr16:70780120-70780130
29	MYC	chr16:70779339-70781016	A549	lung:	n/a	chr16:70780147-70780154 chr16:70780788-70780797 chr16:70780789-70780798 chr16:70780144-70780155 chr16:70780406-70780416 chr16:70780145-70780154 chr16:70780120-70780130
30	POLR2A	chr16:70779863-70781247	U87	brain:	n/a	n/a
31	STAT3	chr16:70779831-70781250	MCF10A-Er-Src	breast:	n/a	chr16:70780773-70780785 chr16:70780110-70780122 chr16:70780788-70780797 chr16:70780789-70780798
32	SP1	chr16:70779630-70781166	A549	lung:	n/a	chr16:70780118-70780132 chr16:70780119-70780128 chr16:70780772-70780786
33	JUND	chr16:70780005-70781040	A549	lung:	n/a	chr16:70780787-70780798 chr16:70780350-70780359 chr16:70780787-70780799 chr16:70780788-70780797 chr16:70780789-70780798 chr16:70780789-70780797 chr16:70780789-70780796 chr16:70780349-70780358
34	TBP	chr16:70780029-70781135	HepG2	liver:	n/a	n/a
35	FOS	chr16:70779962-70781247	MCF10A-Er-Src	breast:	n/a	chr16:70780350-70780359 chr16:70780787-70780799 chr16:70780788-70780797 chr16:70780789-70780798 chr16:70780789-70780797 chr16:70780787-70780798 chr16:70780789-70780796 chr16:70780349-70780358
36	JUND	chr16:70780050-70781109	MCF-7	breast:	n/a	chr16:70780787-70780798 chr16:70780350-70780359 chr16:70780787-70780799 chr16:70780788-70780797 chr16:70780789-70780798 chr16:70780789-70780797 chr16:70780789-70780796 chr16:70780349-70780358
37	RCOR1	chr16:70779984-70781261	HepG2	liver:	n/a	n/a
38	MYC	chr16:70779962-70781286	HepG2	liver:	n/a	chr16:70780147-70780154 chr16:70780788-70780797 chr16:70780789-70780798 chr16:70780144-70780155 chr16:70780406-70780416 chr16:70780145-70780154 chr16:70780120-70780130
39	HDAC2	chr16:70779607-70781372	HepG2	liver:	n/a	n/a
40	POLR2A	chr16:70780089-70780274	A549	lung:	n/a	n/a
41	MAX	chr16:70779747-70782130	NB4	blood:	n/a	chr16:70780147-70780154 chr16:70780788-70780797 chr16:70781664-70781673 chr16:70780789-70780798 chr16:70780144-70780155 chr16:70780406-70780416 chr16:70781665-70781672 chr16:70780145-70780154 chr16:70781663-70781673 chr16:70780120-70780130
42	PBX3	chr16:70780085-70780245	GM12878	blood:	n/a	n/a
43	RFX5	chr16:70779969-70781273	HepG2	liver:	n/a	n/a
44	HEY1	chr16:70779949-70781419	HepG2	liver:	n/a	n/a
45	TEAD4	chr16:70779554-70781514	HepG2	liver:	n/a	n/a
46	BRCA1	chr16:70780022-70780866	HepG2	liver:	n/a	n/a
47	NFIC	chr16:70779952-70781152	ECC-1	luminal epithelium:	n/a	n/a
48	MXI1	chr16:70779515-70781281	IMR90	lung:	n/a	chr16:70779797-70779806 chr16:70780407-70780416
49	POLR2A	chr16:70780034-70781009	HepG2	liver:	n/a	n/a
50	HNF4G	chr16:70779848-70780417	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:70728939..70732766-chr16:70778342..70782420,7	MCF-7	breast:
2	chr16:70716977..70719990-chr16:70779925..70783515,4	K562	blood:
3	chr16:70715424..70721545-chr16:70778213..70783786,16	MCF-7	breast:
4	chr16:70733046..70734873-chr16:70779967..70781686,2	MCF-7	breast:
5	chr16:70726776..70729774-chr16:70778926..70781727,2	K562	blood:
6	chr16:70728125..70734937-chr16:70778355..70783574,11	MCF-7	breast:
7	chr16:70716857..70722605-chr16:70776377..70783146,15	MCF-7	breast:
8	chr16:70779313..70782251-chr16:70793446..70796523,4	K562	blood:
9	chr16:70710951..70713595-chr16:70779027..70782774,3	MCF-7	breast:
10	chr16:70556680..70559302-chr16:70779045..70781738,2	MCF-7	breast:
11	chr16:70716977..70720923-chr16:70779925..70783515,4	K562	blood:
12	chr16:70713469..70715146-chr16:70778729..70780747,2	MCF-7	breast:

Variant related genes	Relation type
VAC14	TF binding region
ENSG00000260156	TF binding region
ENSG00000132613	Chromatin interaction
ENSG00000103051	Chromatin interaction
ENSG00000103043	Chromatin interaction
ENSG00000189091	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12149236	0.85[ASN][1000 genomes]
rs16970484	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16970513	1.00[CEU][hapmap];0.86[MEX][hapmap]
rs17248914	1.00[CEU][hapmap]
rs17307409	1.00[JPT][hapmap]
rs2290614	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[ASN][1000 genomes]
rs2305688	0.82[MEX][hapmap]
rs2902830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3743988	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.94[ASN][1000 genomes]
rs3760118	1.00[CEU][hapmap]
rs3785421	0.94[ASN][1000 genomes]
rs4985364	0.93[CEU][hapmap]
rs4985423	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs60028268	0.91[ASN][1000 genomes]
rs6499336	0.86[CEU][hapmap]
rs7185187	0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[ASN][1000 genomes]
rs7185921	1.00[CEU][hapmap];0.86[MEX][hapmap]
rs7188712	0.92[CEU][hapmap]
rs7190561	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7194091	1.00[CEU][hapmap];0.80[MEX][hapmap]
rs7203578	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[ASN][1000 genomes]
rs7205738	0.84[ASN][1000 genomes]
rs8052615	0.81[CEU][hapmap];0.80[MEX][hapmap]
rs8060947	0.93[CEU][hapmap];0.86[MEX][hapmap]
rs9931380	0.81[CEU][hapmap]
rs9939763	1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517391	chr16:70666410-70840490	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv457517	chr16:70666722-70840490	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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 target site	30 gene(s)	inside rSNPs	diseases
3	nsv572945	chr16:70666722-70840490	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv906878	chr16:70677785-70782922	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS 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	19 gene(s)	inside rSNPs	diseases
5	nsv906879	chr16:70677785-70790831	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS 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 lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv906880	chr16:70677785-70796515	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers 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 target site	20 gene(s)	inside rSNPs	diseases
7	nsv906889	chr16:70724001-70790831	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv906890	chr16:70740707-70790831	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1061191	chr16:70754975-71201367	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
10	nsv1059478	chr16:70773597-71237055	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6499335	TPPP3	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70760000-70784200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr16:70771200-70782000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr16:70771400-70783800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:70772400-70783000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr16:70772600-70813400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr16:70773000-70805600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr16:70773000-70815800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr16:70773400-70816200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr16:70774200-70780600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr16:70775200-70780800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr16:70775800-70782600	Weak transcription	Fetal Kidney	kidney
12	chr16:70776200-70780200	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr16:70777400-70780800	Strong transcription	H9 Cell Line	embryonic stem cell
14	chr16:70777400-70784400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr16:70777600-70781200	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr16:70777800-70780400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr16:70777800-70780400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr16:70777800-70783800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr16:70777800-70783800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr16:70777800-70788400	Enhancers	Psoas Muscle	Psoas
21	chr16:70778200-70782600	Genic enhancers	Spleen	Spleen
22	chr16:70778200-70784400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr16:70778400-70780600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr16:70778400-70788200	Enhancers	Liver	Liver
25	chr16:70778600-70780200	Weak transcription	Brain Germinal Matrix	brain
26	chr16:70778600-70780200	Weak transcription	GM12878-XiMat	blood
27	chr16:70778600-70783600	Enhancers	HSMMtube	muscle
28	chr16:70778600-70784000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr16:70778600-70784000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr16:70778600-70785000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr16:70778800-70780200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr16:70778800-70781800	Enhancers	Stomach Mucosa	stomach
33	chr16:70778800-70783600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr16:70778800-70784000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr16:70778800-70787000	Enhancers	Fetal Thymus	thymus
36	chr16:70778800-70788000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr16:70779000-70782600	Enhancers	Right Ventricle	heart
38	chr16:70779000-70783400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr16:70779000-70783800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr16:70779000-70784600	Enhancers	HSMM	muscle
41	chr16:70779000-70785000	Weak transcription	Primary B cells from cord blood	blood
42	chr16:70779000-70786200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr16:70779000-70786400	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr16:70779000-70786400	Enhancers	NHDF-Ad	bronchial
45	chr16:70779000-70788600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr16:70779200-70780200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr16:70779200-70780200	Enhancers	Stomach Smooth Muscle	stomach
48	chr16:70779200-70780400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr16:70779200-70781000	Enhancers	Fetal Brain Male	brain
50	chr16:70779200-70781200	Enhancers	Brain Cingulate Gyrus	brain

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