Variant report

Variant	rs2247216
Chromosome Location	chr19:51307833-51307834
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	SIN3AK20	chr19:51307663-51307957	SK-N-SH	brain:	n/a	n/a
2	ATF3	chr19:51307578-51308060	K562	blood:	n/a	n/a
3	POLR2A	chr19:51307581-51307992	HepG2	liver:	n/a	n/a
4	ZMIZ1	chr19:51307607-51308579	K562	blood:	n/a	n/a
5	POLR2A	chr19:51305171-51308575	Hela-S3	cervix:	n/a	n/a
6	MAX	chr19:51307397-51308657	SK-N-SH	brain:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51308329-51308340
7	POLR2A	chr19:51307494-51308011	SK-N-SH	brain:	n/a	n/a
8	NR2F2	chr19:51307531-51308897	K562	blood:	n/a	n/a
9	E2F6	chr19:51307597-51308028	K562	blood:	n/a	chr19:51307865-51307879 chr19:51307850-51307859
10	MYC	chr19:51307575-51308547	MCF10A-Er-Src	breast:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51308329-51308340
11	ELK1	chr19:51307652-51308538	K562	blood:	n/a	n/a
12	TCF12	chr19:51307651-51308431	ECC-1	luminal epithelium:	n/a	n/a
13	NFIC	chr19:51307479-51308454	HepG2	liver:	n/a	n/a
14	SP1	chr19:51307666-51308578	H1-hESC	embryonic stem cell:	n/a	chr19:51308226-51308235 chr19:51308055-51308062 chr19:51308224-51308236 chr19:51308277-51308291 chr19:51308280-51308292 chr19:51308282-51308291 chr19:51308280-51308292 chr19:51308224-51308236 chr19:51308281-51308290
15	WRNIP1	chr19:51307547-51308490	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:51306817-51308499	MCF-7	breast:	n/a	n/a
17	ARID3A	chr19:51307814-51308412	HepG2	liver:	n/a	n/a
18	CHD2	chr19:51307501-51308595	Hela-S3	cervix:	n/a	chr19:51307601-51307611
19	MAX	chr19:51307546-51308491	H1-hESC	embryonic stem cell:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51308329-51308340
20	RFX5	chr19:51307649-51308588	Hela-S3	cervix:	n/a	n/a
21	MYC	chr19:51307571-51308460	HUVEC	blood vessel:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51308329-51308340
22	MAX	chr19:51306885-51308746	HCT-116	colon:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51307163-51307172 chr19:51308329-51308340
23	POLR2A	chr19:51307626-51308142	HepG2	liver:	n/a	n/a
24	SIN3AK20	chr19:51307480-51308417	A549	lung:	n/a	n/a
25	ETS1	chr19:51307517-51308461	K562	blood:	n/a	chr19:51307795-51307804 chr19:51308375-51308384
26	PAX5	chr19:51307503-51308034	GM12892	blood:	n/a	n/a
27	SP1	chr19:51307688-51308471	K562	blood:	n/a	chr19:51308226-51308235 chr19:51308055-51308062 chr19:51308224-51308236 chr19:51308277-51308291 chr19:51308280-51308292 chr19:51308282-51308291 chr19:51308280-51308292 chr19:51308224-51308236 chr19:51308281-51308290
28	POU2F2	chr19:51307631-51307960	GM12878	blood:	n/a	n/a
29	REST	chr19:51307691-51307900	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr19:51307239-51308586	SK-N-MC	brain:	n/a	n/a
31	TAF1	chr19:51307329-51308544	K562	blood:	n/a	n/a
32	ZNF384	chr19:51307744-51308313	K562	blood:	n/a	n/a
33	PAX5	chr19:51307569-51308404	GM12878	blood:	n/a	n/a
34	CEBPB	chr19:51307736-51308617	ECC-1	luminal epithelium:	n/a	chr19:51307784-51307796
35	NFIC	chr19:51307745-51308275	HepG2	liver:	n/a	n/a
36	TAF1	chr19:51307381-51308294	Hela-S3	cervix:	n/a	n/a
37	CREB1	chr19:51307494-51308675	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:51306345-51308647	HL-60	blood:	n/a	n/a
39	BCL3	chr19:51306668-51308338	A549	lung:	n/a	chr19:51307558-51307571 chr19:51307558-51307567 chr19:51307959-51307968 chr19:51307280-51307289
40	FOXM1	chr19:51307493-51308511	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:51305218-51308754	SK-N-MC	brain:	n/a	n/a
42	TAF1	chr19:51307450-51308010	GM12891	blood:	n/a	n/a
43	REST	chr19:51307232-51308752	H1-neurons	neurons:	n/a	chr19:51308032-51308039 chr19:51308032-51308052 chr19:51307571-51307584 chr19:51308032-51308052
44	JUND	chr19:51307588-51308357	A549	lung:	n/a	n/a
45	MAX	chr19:51306993-51308542	K562	blood:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51307163-51307172 chr19:51308329-51308340
46	TAF1	chr19:51307205-51308602	H1-hESC	embryonic stem cell:	n/a	n/a
47	POU2F2	chr19:51307489-51308489	GM12891	blood:	n/a	chr19:51308278-51308290 chr19:51308220-51308232
48	ATF2	chr19:51307529-51308448	GM12878	blood:	n/a	n/a
49	TAF1	chr19:51307368-51308036	GM12878	blood:	n/a	n/a
50	REST	chr19:51307487-51307987	SK-N-SH	brain:	n/a	chr19:51307571-51307584

No.	Distal block	Cell Line	Cell type
1	chr19:51306486..51308352-chr19:51377900..51380168,3	K562	blood:
2	chr17:7747918..7748885-chr19:51307437..51308237,2	Hela-S3	cervix:
3	chr19:51225685..51229614-chr19:51306371..51310193,7	MCF-7	breast:
4	chr15:100888968..100891280-chr19:51305902..51308003,2	MCF-7	breast:
5	chr19:51306616..51308250-chr19:51611321..51612835,2	K562	blood:
6	chr19:51306849..51308707-chr19:51324714..51327546,2	MCF-7	breast:
7	chr19:51307483..51308026-chr3:32611910..32612463,2	Hela-S3	cervix:
8	chr19:50878289..50880426-chr19:51306206..51308776,2	K562	blood:
9	chr19:51304876..51308314-chr19:51372660..51375800,4	MCF-7	breast:
10	chr19:51225811..51229710-chr19:51304326..51309315,7	K562	blood:
11	chr17:7387524..7388142-chr19:51307662..51308292,2	HCT-116	colon:
12	chr19:51305915..51308029-chr19:51455480..51457752,2	K562	blood:
13	chr19:51307346..51307950-chr2:25194320..25194911,2	Hela-S3	cervix:
14	chr19:51291032..51294383-chr19:51305809..51308243,6	MCF-7	breast:
15	chr12:120729226..120729925-chr19:51307414..51308024,2	Hela-S3	cervix:
16	chr19:51306828..51309257-chr19:51411309..51414080,2	MCF-7	breast:
17	chr19:51221053..51222783-chr19:51305600..51307865,2	K562	blood:
18	chr19:51161291..51162823-chr19:51306692..51308386,2	K562	blood:
19	chr19:51306795..51309015-chr19:51522024..51524887,2	K562	blood:
20	chr19:51306219..51311443-chr19:51320268..51326410,9	MCF-7	breast:
21	chr12:96793648..96794758-chr19:51307794..51308653,3	Hela-S3	cervix:
22	chr14:70233572..70234808-chr19:51306783..51308006,3	Hela-S3	cervix:
23	chr19:51306448..51310717-chr19:51372415..51375235,4	K562	blood:
24	chr19:51306094..51308089-chr20:55841025..55842580,2	MCF-7	breast:
25	chr19:51306173..51309320-chr19:51331029..51336004,5	MCF-7	breast:
26	chr19:51305829..51307927-chr19:51320436..51323745,3	MCF-7	breast:
27	chr19:51307008..51307924-chr3:33481967..33482752,2	NB4	blood:
28	chr19:51306202..51308468-chr19:51372838..51375377,2	K562	blood:
29	chr19:51014538..51017258-chr19:51306499..51308230,2	K562	blood:
30	chr19:50878669..50883054-chr19:51306301..51308717,4	MCF-7	breast:
31	chr1:173836321..173837254-chr19:51307613..51308582,2	Hela-S3	cervix:
32	chr19:51305954..51309003-chr19:51339405..51341608,4	K562	blood:
33	chr19:51305909..51308309-chr19:51411302..51414101,3	MCF-7	breast:

Variant related genes	Relation type
SNORD88C	TF binding region
C19orf48	TF binding region
ENSG00000131408	Chromatin interaction
ENSG00000167749	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000235034	Chromatin interaction
ENSG00000144635	Chromatin interaction
ENSG00000142513	Chromatin interaction
ENSG00000142544	Chromatin interaction
ENSG00000059758	Chromatin interaction
ENSG00000105472	Chromatin interaction
ENSG00000180279	Chromatin interaction
ENSG00000132510	Chromatin interaction
ENSG00000100650	Chromatin interaction
ENSG00000267880	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000204653	Chromatin interaction
ENSG00000129451	Chromatin interaction
ENSG00000167751	Chromatin interaction
ENSG00000161677	Chromatin interaction
ENSG00000115137	Chromatin interaction
ENSG00000167748	Chromatin interaction
ENSG00000161681	Chromatin interaction
ENSG00000174562	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000153560	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000167754	Chromatin interaction
ENSG00000267968	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000189419	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10412900	1.00[JPT][hapmap]
rs17800375	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs2659060	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap]
rs2659063	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs2659064	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs266112	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs266121	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs266124	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs3212855	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs3810283	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
6	nsv526232	chr19:51301230-51335943	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51305800-51309000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr19:51306000-51308600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:51306000-51308600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:51306000-51309000	Active TSS	Colonic Mucosa	Colon
5	chr19:51306200-51308200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr19:51306200-51308600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:51306200-51308600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:51306200-51308600	Active TSS	Fetal Intestine Large	intestine
9	chr19:51306200-51308800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:51306200-51308800	Active TSS	NHLF	lung
11	chr19:51306400-51308600	Active TSS	Esophagus	oesophagus
12	chr19:51306400-51308800	Active TSS	H1 Cell Line	embryonic stem cell
13	chr19:51306400-51308800	Active TSS	H9 Cell Line	embryonic stem cell
14	chr19:51306400-51308800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:51306400-51308800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:51306400-51308800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:51306400-51308800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:51306400-51309000	Active TSS	GM12878-XiMat	blood
19	chr19:51306600-51308600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:51306600-51308600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:51306600-51308600	Active TSS	Fetal Intestine Small	intestine
22	chr19:51306600-51308800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:51306600-51308800	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr19:51306600-51308800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:51306600-51308800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:51306600-51308800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:51306600-51308800	Active TSS	Fetal Kidney	kidney
28	chr19:51306600-51308800	Active TSS	NH-A	brain
29	chr19:51306600-51308800	Active TSS	NHDF-Ad	bronchial
30	chr19:51306800-51308000	Active TSS	Fetal Thymus	thymus
31	chr19:51306800-51308200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:51306800-51308400	Active TSS	HMEC	breast
33	chr19:51306800-51308600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr19:51306800-51308600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr19:51306800-51308600	Active TSS	Ovary	ovary
36	chr19:51306800-51308800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:51307000-51308200	Bivalent/Poised TSS	HepG2	liver
38	chr19:51307000-51308400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:51307000-51308600	Active TSS	Muscle Satellite Cultured Cells	--
40	chr19:51307000-51308600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:51307000-51308600	Active TSS	Hela-S3	cervix
42	chr19:51307000-51308800	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr19:51307000-51308800	Active TSS	Fetal Lung	lung
44	chr19:51307000-51309000	Active TSS	K562	blood
45	chr19:51307200-51308000	Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr19:51307200-51308000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
47	chr19:51307200-51308000	Active TSS	Stomach Mucosa	stomach
48	chr19:51307200-51308200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr19:51307200-51308400	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr19:51307200-51308400	Active TSS	Primary T regulatory cells fromperipheralblood	blood

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