Variant report

Variant	rs2917670
Chromosome Location	chr16:69758963-69758964
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:69757538-69761443	HepG2	liver:	n/a	n/a
2	POLR2A	chr16:69758933-69759511	HepG2	liver:	n/a	n/a
3	FOXA2	chr16:69758952-69759393	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:69758784-69762098	Hela-S3	cervix:	n/a	n/a
5	HEY1	chr16:69758796-69761112	HepG2	liver:	n/a	n/a
6	HEY1	chr16:69758446-69761187	HepG2	liver:	n/a	n/a
7	TEAD4	chr16:69758753-69759409	HepG2	liver:	n/a	n/a
8	POLR2A	chr16:69758854-69759182	HUVEC	blood vessel:	n/a	n/a
9	ZMIZ1	chr16:69758814-69759340	K562	blood:	n/a	n/a
10	HDAC2	chr16:69758909-69759503	K562	blood:	n/a	n/a
11	FOXA1	chr16:69758874-69759352	HepG2	liver:	n/a	n/a
12	POLR2A	chr16:69758775-69759491	MCF10A-Er-Src	breast:	n/a	n/a
13	SIN3A	chr16:69758884-69759195	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr16:69758492-69759584	HepG2	liver:	n/a	n/a
15	SMC3	chr16:69758915-69759107	HepG2	liver:	n/a	n/a
16	SIN3AK20	chr16:69758707-69759143	A549	lung:	n/a	n/a
17	POLR2A	chr16:69758539-69761198	HepG2	liver:	n/a	n/a
18	TBP	chr16:69758734-69759541	HepG2	liver:	n/a	n/a
19	TCF12	chr16:69758736-69761990	A549	lung:	n/a	n/a
20	POLR2A	chr16:69758931-69761864	MCF-7	breast:	n/a	n/a
21	MYBL2	chr16:69758711-69759756	HepG2	liver:	n/a	n/a
22	RCOR1	chr16:69758848-69761598	K562	blood:	n/a	n/a
23	MAX	chr16:69758656-69759005	HepG2	liver:	n/a	n/a
24	POLR2A	chr16:69758874-69759555	HepG2	liver:	n/a	n/a
25	MBD4	chr16:69758545-69759574	HepG2	liver:	n/a	n/a
26	POLR2A	chr16:69758605-69759650	A549	lung:	n/a	n/a
27	POLR2A	chr16:69758963-69761404	HCT-116	colon:	n/a	n/a
28	POLR2A	chr16:69758793-69759595	HepG2	liver:	n/a	n/a
29	SIN3AK20	chr16:69758886-69761355	MCF-7	breast:	n/a	n/a
30	ATF3	chr16:69758571-69759148	A549	lung:	n/a	n/a
31	MYBL2	chr16:69758309-69761134	HepG2	liver:	n/a	n/a
32	STAT3	chr16:69758924-69759124	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr16:69758615-69759511	HepG2	liver:	n/a	n/a
34	SIN3AK20	chr16:69758614-69759183	A549	lung:	n/a	n/a
35	MXI1	chr16:69758867-69759185	HepG2	liver:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:69755811..69761889-chr16:69791851..69798633,14	K562	blood:
2	chr16:69599623..69601716-chr16:69757663..69760565,3	MCF-7	breast:
3	chr16:69758127..69765240-chr16:69786072..69790209,13	K562	blood:
4	chr16:69741703..69743553-chr16:69758543..69761964,3	MCF-7	breast:
5	chr16:69363088..69367214-chr16:69757729..69760450,3	MCF-7	breast:
6	chr16:69757296..69762552-chr16:69785671..69789636,11	K562	blood:
7	chr16:69757781..69759922-chr16:69795313..69797984,2	MCF-7	breast:
8	chr16:69756628..69762611-chr16:69781362..69792848,24	MCF-7	breast:
9	chr16:69757858..69760516-chr16:69796168..69797980,2	MCF-7	breast:
10	chr16:69757413..69759296-chr16:69767966..69769499,2	K562	blood:
11	chr16:69758592..69760994-chr16:70729394..70731021,2	K562	blood:
12	chr16:69756715..69759145-chr16:69764152..69766520,2	MCF-7	breast:
13	chr16:69741680..69751385-chr16:69755023..69763559,18	MCF-7	breast:
14	chr16:69756730..69759339-chr16:69925366..69928011,2	K562	blood:
15	chr15:75931960..75934199-chr16:69758900..69760428,2	K562	blood:
16	chr16:69756797..69758977-chr16:69893050..69895419,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000262136	TF binding region
ENSG00000223109	Chromatin interaction
ENSG00000261602	Chromatin interaction
ENSG00000260290	Chromatin interaction
ENSG00000177971	Chromatin interaction
ENSG00000258429	Chromatin interaction
ENSG00000141101	Chromatin interaction
ENSG00000198373	Chromatin interaction
ENSG00000102908	Chromatin interaction
ENSG00000238683	Chromatin interaction
ENSG00000103043	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11640319	0.85[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs12596945	0.81[ASN][1000 genomes]
rs12599391	0.87[LWK][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap]
rs12918548	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12921782	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12924052	0.96[CEU][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12933210	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1364063	0.87[LWK][hapmap];0.88[MKK][hapmap];0.95[YRI][hapmap]
rs1437134	0.87[LWK][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap]
rs1469908	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1837016	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2017448	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2161630	0.85[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs244415	0.87[LWK][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap]
rs244417	0.87[LWK][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap]
rs244418	0.87[LWK][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap]
rs244420	0.87[LWK][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap]
rs2917671	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917677	0.82[AFR][1000 genomes]
rs2917678	0.86[ASN][1000 genomes]
rs2965749	0.84[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];0.86[ASN][1000 genomes]
rs3811348	0.96[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3848278	0.85[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs45488899	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4633710	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.84[ASN][1000 genomes]
rs55780735	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6499241	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6499244	0.89[YRI][hapmap]
rs7186296	0.84[JPT][hapmap]
rs7187634	0.85[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7189878	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7191292	0.85[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7192380	0.85[ASW][hapmap];0.88[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7359336	0.87[LWK][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap]
rs8045432	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8049728	0.85[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8055756	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8061052	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9302604	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs9938213	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	54 gene(s)	inside rSNPs	diseases
2	esv3396845	chr16:69721905-69770627	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv517207	chr16:69745145-69771914	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv524364	chr16:69745145-69803443	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2917670	TPPP3	cis	cerebellum	SCAN
rs2917670	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs2917670	PLEKHG4	cis	parietal	SCAN
rs2917670	HSF4	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69726600-69759800	Weak transcription	Psoas Muscle	Psoas
2	chr16:69728400-69759200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:69729400-69760000	Weak transcription	Brain Germinal Matrix	brain
4	chr16:69729400-69760000	Weak transcription	Ovary	ovary
5	chr16:69730000-69759000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr16:69730600-69759800	Weak transcription	Fetal Brain Female	brain
7	chr16:69730800-69759800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr16:69731800-69759600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr16:69731800-69759800	Weak transcription	Primary B cells from cord blood	blood
10	chr16:69731800-69759800	Weak transcription	Right Ventricle	heart
11	chr16:69733800-69759800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr16:69738800-69759800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr16:69739200-69759800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr16:69741000-69759200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr16:69741000-69759400	Weak transcription	Small Intestine	intestine
16	chr16:69741600-69759800	Weak transcription	Primary T cells from cord blood	blood
17	chr16:69743800-69760000	Weak transcription	Fetal Kidney	kidney
18	chr16:69744000-69759800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr16:69745400-69759800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr16:69747000-69759000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr16:69747200-69759600	Weak transcription	Thymus	Thymus
22	chr16:69747400-69759200	Weak transcription	Spleen	Spleen
23	chr16:69747400-69759400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr16:69747400-69759800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr16:69747400-69759800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr16:69749400-69759000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr16:69749400-69759200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr16:69749400-69759200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr16:69749400-69759800	Weak transcription	Brain Angular Gyrus	brain
30	chr16:69749400-69760000	Weak transcription	Fetal Lung	lung
31	chr16:69749600-69760000	Weak transcription	Pancreas	Pancrea
32	chr16:69749800-69759800	Weak transcription	Colon Smooth Muscle	Colon
33	chr16:69751400-69759400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr16:69751600-69759000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr16:69751600-69760000	Weak transcription	Liver	Liver
36	chr16:69752200-69759000	Weak transcription	Brain Substantia Nigra	brain
37	chr16:69752200-69759000	Weak transcription	Fetal Muscle Leg	muscle
38	chr16:69752400-69759000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr16:69752400-69759400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr16:69752400-69759800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr16:69752400-69759800	Weak transcription	Esophagus	oesophagus
42	chr16:69752400-69760000	Weak transcription	Aorta	Aorta
43	chr16:69752600-69759200	Weak transcription	Placenta	Placenta
44	chr16:69752600-69759800	Weak transcription	Left Ventricle	heart
45	chr16:69752600-69760000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr16:69752800-69759200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr16:69754600-69759200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr16:69754800-69759600	Transcr. at gene 5' and 3'	A549	lung
49	chr16:69755400-69759400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr16:69755600-69759000	Weak transcription	Gastric	stomach

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