Variant report

Variant	rs17006416
Chromosome Location	chr3:19987804-19987805
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	chr3:19987362-19989595	K562	blood:	n/a	n/a
2	HCFC1	chr3:19987605-19989689	K562	blood:	n/a	n/a
3	RUNX3	chr3:19987795-19989519	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:19987558-19989602	GM18951	blood:	n/a	n/a
5	POLR2A	chr3:19986887-19989909	GM12891	blood:	n/a	n/a
6	SIN3AK20	chr3:19987338-19989938	MCF-7	breast:	n/a	n/a
7	BCL3	chr3:19987604-19988689	A549	lung:	n/a	chr3:19988323-19988332 chr3:19988611-19988624 chr3:19988633-19988642
8	JUN	chr3:19987484-19988866	K562	blood:	n/a	n/a
9	SMARCC1	chr3:19986964-19989766	Hela-S3	cervix:	n/a	chr3:19989188-19989197 chr3:19989189-19989198
10	POLR2A	chr3:19987474-19989718	GM12878	blood:	n/a	n/a
11	FOXM1	chr3:19987637-19989053	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:19987476-19989652	U87	brain:	n/a	n/a
13	POLR2A	chr3:19987594-19989784	GM18505	blood:	n/a	n/a
14	POLR2A	chr3:19987565-19989776	MCF-7	breast:	n/a	n/a
15	POLR2A	chr3:19987429-19989814	H1-hESC	embryonic stem cell:	n/a	n/a
16	TBP	chr3:19986938-19989974	K562	blood:	n/a	n/a
17	MEF2A	chr3:19987741-19988852	GM12878	blood:	n/a	n/a
18	CHD2	chr3:19987637-19989399	H1-hESC	embryonic stem cell:	n/a	chr3:19989363-19989373
19	WRNIP1	chr3:19987590-19989775	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:19987007-19989845	K562	blood:	n/a	n/a
21	POLR2A	chr3:19986884-19989655	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr3:19986589-19991063	MCF10A-Er-Src	breast:	n/a	n/a
23	CEBPB	chr3:19986935-19988000	A549	lung:	n/a	chr3:19987312-19987323 chr3:19987314-19987323 chr3:19987314-19987323 chr3:19987314-19987323 chr3:19987314-19987325 chr3:19987314-19987323
24	RAD21	chr3:19987744-19987887	HepG2	liver:	n/a	chr3:19987822-19987841
25	GATA1	chr3:19987428-19990353	PBDE	blood:	n/a	chr3:19990147-19990157
26	PML	chr3:19987602-19989745	K562	blood:	n/a	chr3:19989187-19989196 chr3:19989190-19989199
27	UBTF	chr3:19987157-19989859	K562	blood:	n/a	n/a
28	MYC	chr3:19986886-19989780	K562	blood:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
29	MAFF	chr3:19986970-19988337	K562	blood:	n/a	n/a
30	ZMIZ1	chr3:19987025-19989940	K562	blood:	n/a	n/a
31	REST	chr3:19987675-19989803	H1-neurons	neurons:	n/a	chr3:19989444-19989457 chr3:19989079-19989092
32	TEAD4	chr3:19987245-19989018	K562	blood:	n/a	n/a
33	MAZ	chr3:19987619-19989864	IMR90	lung:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
34	POLR2A	chr3:19987567-19989872	PBDE	blood:	n/a	n/a
35	CEBPB	chr3:19986878-19988787	K562	blood:	n/a	chr3:19987312-19987323 chr3:19987314-19987323 chr3:19987314-19987323 chr3:19987314-19987323 chr3:19987314-19987325 chr3:19987314-19987323
36	ZNF384	chr3:19986941-19987984	K562	blood:	n/a	n/a
37	CTCF	chr3:19987563-19989811	K562	blood:	n/a	chr3:19989472-19989480 chr3:19987821-19987839 chr3:19989265-19989286 chr3:19989198-19989207
38	TAL1	chr3:19986884-19990195	K562	blood:	n/a	chr3:19989618-19989626
39	POLR2A	chr3:19986679-19989723	MCF10A-Er-Src	breast:	n/a	n/a
40	TBL1XR1	chr3:19987595-19989796	K562	blood:	n/a	n/a
41	POLR2A	chr3:19986941-19989740	Hela-S3	cervix:	n/a	n/a
42	MAFK	chr3:19987652-19988693	Hela-S3	cervix:	n/a	chr3:19988182-19988197
43	PML	chr3:19987740-19989681	GM12878	blood:	n/a	chr3:19989187-19989196 chr3:19989190-19989199
44	CHD1	chr3:19987459-19990325	IMR90	lung:	n/a	chr3:19989363-19989373
45	USF2	chr3:19987523-19988716	Hela-S3	cervix:	n/a	chr3:19988614-19988630 chr3:19988464-19988475
46	POLR2A	chr3:19987273-19989684	GM12878	blood:	n/a	n/a
47	YY1	chr3:19987774-19989636	H1-hESC	embryonic stem cell:	n/a	chr3:19988611-19988625 chr3:19989269-19989277 chr3:19988611-19988620 chr3:19987999-19988008 chr3:19988151-19988159 chr3:19989258-19989280
48	UBTF	chr3:19987082-19989813	K562	blood:	n/a	n/a
49	MYC	chr3:19987657-19989599	NB4	blood:	n/a	chr3:19988609-19988619 chr3:19989189-19989198
50	POLR2A	chr3:19987004-19989709	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:19986921..19992254-chr3:20078952..20084327,16	K562	blood:
2	chr3:19987782..19990680-chr3:20013275..20017779,4	K562	blood:
3	chr17:8076548..8077059-chr3:19987723..19988396,2	Hela-S3	cervix:
4	chr3:19987383..19992426-chr3:20011245..20019650,13	MCF-7	breast:
5	chr3:19987439..19992261-chr3:20226257..20229350,4	K562	blood:
6	chr3:19987513..19990087-chr3:20080861..20083140,3	MCF-7	breast:
7	chr3:19985145..19990136-chr3:20225418..20228312,6	K562	blood:
8	chr3:19975611..19979082-chr3:19987774..19990681,3	MCF-7	breast:
9	chr3:19986985..19992254-chr3:20079680..20083856,14	K562	blood:

Variant related genes	Relation type
HSPA8P18	TF binding region
RAB5A	TF binding region
ENSG00000200463	Chromatin interaction
ENSG00000114166	Chromatin interaction
ENSG00000144566	Chromatin interaction
ENSG00000129810	Chromatin interaction
ENSG00000163576	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10510497	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs12486526	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs12495866	0.90[AFR][1000 genomes]
rs13319903	0.84[AFR][1000 genomes]
rs17006418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17006433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17006435	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17006443	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs28525232	0.84[AFR][1000 genomes]
rs4241539	1.00[ASW][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs4858632	0.90[AFR][1000 genomes]
rs56994247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57181336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57382802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57584064	0.87[AFR][1000 genomes]
rs57771037	0.82[AFR][1000 genomes]
rs58529752	0.82[AFR][1000 genomes]
rs58545026	0.82[AFR][1000 genomes]
rs58731891	0.87[AFR][1000 genomes]
rs59301227	0.87[AFR][1000 genomes]
rs59361244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61255313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61369715	0.82[AFR][1000 genomes]
rs62241286	0.90[AFR][1000 genomes]
rs62241316	0.90[AFR][1000 genomes]
rs62241322	0.90[AFR][1000 genomes]
rs6774670	1.00[AMR][1000 genomes]
rs6802632	0.86[YRI][hapmap]
rs9822900	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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	18 gene(s)	inside rSNPs	diseases
5	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	15 gene(s)	inside rSNPs	diseases
11	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19986800-19988000	Flanking Active TSS	Hela-S3	cervix
2	chr3:19986800-19990200	Active TSS	Duodenum Mucosa	Duodenum
3	chr3:19987000-19989600	Active TSS	Liver	Liver
4	chr3:19987200-19989000	Active TSS	HepG2	liver
5	chr3:19987200-19989800	Active TSS	Pancreas	Pancrea
6	chr3:19987200-19990400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:19987200-19990400	Active TSS	Placenta	Placenta
8	chr3:19987200-19990600	Active TSS	K562	blood
9	chr3:19987200-19991800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr3:19987400-19988000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:19987400-19988000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:19987400-19988000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr3:19987400-19988000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:19987400-19988000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr3:19987400-19988000	Flanking Active TSS	Fetal Intestine Small	intestine
16	chr3:19987400-19988000	Enhancers	Spleen	Spleen
17	chr3:19987400-19988000	Flanking Active TSS	NHEK	skin
18	chr3:19987400-19988200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr3:19987400-19988200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr3:19987400-19988200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:19987400-19988200	Flanking Active TSS	Dnd41	blood
22	chr3:19987400-19988800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:19987400-19989000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:19987400-19989200	Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr3:19987400-19989400	Active TSS	Brain Anterior Caudate	brain
26	chr3:19987400-19989400	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr3:19987400-19989400	Active TSS	Rectal Smooth Muscle	rectum
28	chr3:19987400-19989800	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr3:19987400-19990000	Active TSS	Brain Germinal Matrix	brain
30	chr3:19987400-19990000	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr3:19987400-19990000	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr3:19987400-19990000	Active TSS	A549	lung
33	chr3:19987400-19990200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:19987400-19990200	Active TSS	HSMM	muscle
35	chr3:19987400-19990400	Active TSS	NHDF-Ad	bronchial
36	chr3:19987400-19990800	Active TSS	Right Atrium	heart
37	chr3:19987400-19990800	Active TSS	HSMMtube	muscle
38	chr3:19987400-19991400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:19987600-19988000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
40	chr3:19987600-19988000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr3:19987600-19988000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:19987600-19988000	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:19987600-19988000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr3:19987600-19988000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:19987600-19988000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:19987600-19988000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr3:19987600-19988000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr3:19987600-19988000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:19987600-19988000	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr3:19987600-19988000	Flanking Active TSS	Brain Substantia Nigra	brain

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