Variant report

Variant	rs4141062
Chromosome Location	chr19:42756345-42756346
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	chr19:42755662-42756486	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:42749868-42759399	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:42755613-42758038	MCF-7	breast:	n/a	n/a
4	POLR2A	chr19:42755650-42756357	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:42756013-42756397	U87	brain:	n/a	n/a
6	POLR2A	chr19:42755692-42757890	IMR90	lung:	n/a	n/a
7	MAZ	chr19:42754805-42760905	IMR90	lung:	n/a	chr19:42759369-42759378 chr19:42755056-42755065 chr19:42756308-42756319 chr19:42758228-42758238 chr19:42759385-42759395 chr19:42758595-42758605 chr19:42757003-42757010 chr19:42757000-42757013 chr19:42757002-42757011 chr19:42760033-42760042 chr19:42757284-42757293 chr19:42757002-42757012 chr19:42759330-42759339 chr19:42759102-42759117 chr19:42758566-42758576 chr19:42758254-42758264 chr19:42757001-42757012 chr19:42759119-42759129 chr19:42759365-42759374
8	POLR2A	chr19:42756006-42756487	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr19:42756183-42756381	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:42755854-42756501	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr19:42755675-42757964	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:42755770-42757895	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:42755650-42756486	HepG2	liver:	n/a	n/a
14	JUND	chr19:42755961-42759795	A549	lung:	n/a	chr19:42758772-42758781 chr19:42758914-42758925 chr19:42757598-42757607 chr19:42758776-42758785 chr19:42756903-42756912 chr19:42757152-42757163 chr19:42758256-42758265 chr19:42758594-42758603
15	ZBTB7A	chr19:42756133-42756594	K562	blood:	n/a	chr19:42756491-42756505
16	POLR2A	chr19:42756004-42756370	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr19:42756122-42757507	K562	blood:	n/a	n/a
18	MXI1	chr19:42756154-42758085	IMR90	lung:	n/a	n/a
19	POLR2A	chr19:42746451-42758038	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr19:42755739-42757855	A549	lung:	n/a	n/a
21	BCL3	chr19:42755761-42757986	A549	lung:	n/a	chr19:42756711-42756719 chr19:42757432-42757441
22	POLR2A	chr19:42748210-42757941	K562	blood:	n/a	n/a
23	SIN3AK20	chr19:42755649-42756371	A549	lung:	n/a	n/a
24	PBX3	chr19:42755733-42757876	A549	lung:	n/a	chr19:42756451-42756462
25	TCF12	chr19:42755643-42761138	A549	lung:	n/a	chr19:42758939-42758947 chr19:42757723-42757733 chr19:42757546-42757554 chr19:42758133-42758143 chr19:42759581-42759591 chr19:42756589-42756599 chr19:42757196-42757203
26	STAT5A	chr19:42755818-42756486	GM12878	blood:	n/a	n/a
27	MXI1	chr19:42755825-42757950	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr19:42755671-42757972	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr19:42754993-42759794	K562	blood:	n/a	n/a
30	POLR2A	chr19:42749752-42759489	K562	blood:	n/a	n/a
31	REST	chr19:42755664-42757949	A549	lung:	n/a	chr19:42757808-42757818 chr19:42756712-42756725 chr19:42755665-42755675 chr19:42756712-42756721 chr19:42756715-42756728
32	POLR2A	chr19:42748038-42760873	SK-N-MC	brain:	n/a	n/a
33	ZBTB7A	chr19:42756197-42757009	K562	blood:	n/a	chr19:42756491-42756505

No.	Distal block	Cell Line	Cell type
1	chr19:42754219..42757685-chr19:42805206..42807524,5	MCF-7	breast:
2	chr19:42747132..42763787-chr19:42768368..42776785,67	MCF-7	breast:
3	chr19:42719999..42721511-chr19:42755568..42757404,2	MCF-7	breast:
4	chr19:42754290..42756701-chr19:42804402..42806386,2	K562	blood:
5	chr19:42744297..42761073-chr19:42776978..42802286,113	MCF-7	breast:
6	chr19:42755150..42756670-chr19:42837239..42839468,2	K562	blood:
7	chr19:42755773..42757418-chr7:73245264..73246953,2	MCF-7	breast:
8	chr19:42756164..42759141-chr5:40680173..40681787,2	MCF-7	breast:
9	chr19:42743599..42762610-chr19:42780302..42801550,102	MCF-7	breast:

Variant related genes	Relation type
ERF	TF binding region
ENSG00000079432	Chromatin interaction
ENSG00000188368	Chromatin interaction
ENSG00000079462	Chromatin interaction
ENSG00000171522	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10410185	1.00[CHB][hapmap];0.80[MEX][hapmap];0.95[ASN][1000 genomes]
rs10410198	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs10410698	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs10412833	0.86[ASN][1000 genomes]
rs10426306	0.95[ASN][1000 genomes]
rs10426310	0.95[ASN][1000 genomes]
rs10500285	0.86[GIH][hapmap]
rs11557114	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11878620	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11880124	0.82[CHB][hapmap];0.86[GIH][hapmap]
rs11882654	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11883412	0.82[CHB][hapmap];0.89[GIH][hapmap];0.80[MEX][hapmap]
rs1206009	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1206027	1.00[CHB][hapmap]
rs1206029	1.00[CHB][hapmap];0.80[MEX][hapmap]
rs1206033	1.00[CHB][hapmap]
rs1206038	1.00[CHB][hapmap]
rs1206040	1.00[CHB][hapmap]
rs1206041	1.00[CHB][hapmap]
rs1206044	1.00[CHB][hapmap]
rs1209280	0.86[ASN][1000 genomes]
rs1211265	0.86[ASN][1000 genomes]
rs1613100	1.00[CHB][hapmap]
rs1654623	1.00[CHB][hapmap]
rs1676211	1.00[CHB][hapmap]
rs1676217	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1676221	1.00[CHB][hapmap]
rs1676222	1.00[CHB][hapmap]
rs1685565	1.00[CHB][hapmap]
rs16975684	0.82[CHB][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap]
rs17270169	0.86[GIH][hapmap];1.00[YRI][hapmap]
rs2267630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2302485	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2303652	0.82[CHB][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap]
rs2537697	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2615614	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs28537976	0.95[ASN][1000 genomes]
rs28621009	1.00[CHB][hapmap]
rs35493131	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3745231	0.82[CHB][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap]
rs3745233	0.82[CHB][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap]
rs3810148	1.00[CHB][hapmap];0.80[MEX][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3810151	0.82[CHB][hapmap]
rs3826705	0.86[GIH][hapmap]
rs57938324	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61735151	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248379	0.82[CHB][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap]
rs7258795	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73552881	0.95[ASN][1000 genomes]
rs73552895	0.95[ASN][1000 genomes]
rs741070	1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8182491	0.82[CHB][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap]
rs851296	1.00[CHB][hapmap]
rs851612	0.91[ASN][1000 genomes]
rs851615	0.86[ASN][1000 genomes]
rs9636121	1.00[CHB][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
7	nsv833833	chr19:42657276-42783122	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
9	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
10	nsv833834	chr19:42736444-42835027	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	42 gene(s)	inside rSNPs	diseases
11	nsv911784	chr19:42741124-42787664	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
12	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
13	nsv911786	chr19:42744234-42797959	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	39 gene(s)	inside rSNPs	diseases
14	esv1802977	chr19:42754437-42789945	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	31 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	chr19:42749000-42757000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:42752600-42757400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:42753600-42756400	Genic enhancers	Spleen	Spleen
4	chr19:42753800-42757000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr19:42753800-42757800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:42754000-42756600	Enhancers	Left Ventricle	heart
7	chr19:42754200-42756800	Enhancers	Esophagus	oesophagus
8	chr19:42754200-42757200	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr19:42754200-42757400	Flanking Active TSS	Brain Germinal Matrix	brain
10	chr19:42754200-42757800	Transcr. at gene 5' and 3'	A549	lung
11	chr19:42754400-42756400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:42754400-42756600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr19:42754400-42757000	Enhancers	Stomach Mucosa	stomach
14	chr19:42754400-42757200	Enhancers	Small Intestine	intestine
15	chr19:42754400-42757600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr19:42754400-42757800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:42754400-42757800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:42754600-42756400	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr19:42754600-42756400	Flanking Active TSS	HSMM	muscle
20	chr19:42754600-42756400	Transcr. at gene 5' and 3'	NHEK	skin
21	chr19:42754600-42756800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr19:42754600-42756800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:42754600-42757000	Enhancers	Placenta Amnion	Placenta Amnion
24	chr19:42754600-42757200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:42754600-42757200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:42754600-42757400	Flanking Active TSS	HMEC	breast
27	chr19:42754600-42757400	Flanking Active TSS	HUVEC	blood vessel
28	chr19:42754600-42757400	Flanking Active TSS	Osteobl	bone
29	chr19:42754600-42757800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:42754800-42756600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr19:42754800-42756600	Weak transcription	Aorta	Aorta
32	chr19:42754800-42756600	Enhancers	Liver	Liver
33	chr19:42754800-42756600	Enhancers	Placenta	Placenta
34	chr19:42754800-42756800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:42754800-42756800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr19:42754800-42756800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr19:42754800-42756800	Enhancers	Lung	lung
38	chr19:42754800-42757000	Enhancers	Primary B cells from peripheral blood	blood
39	chr19:42754800-42757200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
40	chr19:42754800-42757600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr19:42754800-42757800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr19:42755000-42756600	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr19:42755000-42756800	Enhancers	H1 Cell Line	embryonic stem cell
44	chr19:42755000-42757000	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr19:42755000-42757000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:42755000-42757000	Enhancers	Gastric	stomach
47	chr19:42755000-42757200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr19:42755000-42757200	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr19:42755000-42757400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:42755000-42757400	Flanking Active TSS	Right Ventricle	heart

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