Variant report

Variant	rs2604879
Chromosome Location	chr19:41195279-41195280
allele	A/G
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	chr19:41195160-41195740	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr19:41195012-41195701	U87	brain:	n/a	n/a
3	POLR2A	chr19:41195254-41195701	A549	lung:	n/a	n/a
4	POLR2A	chr19:41194751-41195734	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr19:41195015-41196330	U87	brain:	n/a	n/a
6	BCL3	chr19:41194296-41195647	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:41195273-41195661	A549	lung:	n/a	n/a
8	POLR2A	chr19:41195218-41195440	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr19:41195245-41195440	HepG2	liver:	n/a	n/a
10	MTA3	chr19:41195156-41195642	GM12878	blood:	n/a	n/a
11	STAT5A	chr19:41193052-41195402	K562	blood:	n/a	n/a
12	MAX	chr19:41194834-41195723	K562	blood:	n/a	n/a
13	POLR2A	chr19:41195198-41198305	A549	lung:	n/a	n/a
14	POLR2A	chr19:41195136-41198654	K562	blood:	n/a	n/a
15	POLR2A	chr19:41193287-41197366	IMR90	lung:	n/a	n/a
16	MAZ	chr19:41194429-41197886	IMR90	lung:	n/a	chr19:41197262-41197271 chr19:41197258-41197273 chr19:41197265-41197275 chr19:41197260-41197269 chr19:41197261-41197268 chr19:41197251-41197267
17	POLR2A	chr19:41194826-41196977	H1-neurons	neurons:	n/a	n/a
18	MXI1	chr19:41192631-41197581	IMR90	lung:	n/a	chr19:41193038-41193053 chr19:41193021-41193036
19	UBTF	chr19:41195164-41195681	K562	blood:	n/a	n/a
20	MXI1	chr19:41193489-41197689	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr19:41195155-41197968	K562	blood:	n/a	n/a
22	PBX3	chr19:41194601-41195405	GM12878	blood:	n/a	chr19:41195069-41195078
23	POLR2A	chr19:41195216-41195525	H1-hESC	embryonic stem cell:	n/a	n/a
24	TCF12	chr19:41194749-41197918	A549	lung:	n/a	chr19:41197131-41197138
25	PBX3	chr19:41195253-41197574	A549	lung:	n/a	chr19:41196611-41196620
26	MAX	chr19:41194363-41197840	A549	lung:	n/a	chr19:41197262-41197271 chr19:41197258-41197273 chr19:41197265-41197275 chr19:41197260-41197269 chr19:41197261-41197268 chr19:41197251-41197267 chr19:41194393-41194403
27	POLR2A	chr19:41195270-41197954	H1-hESC	embryonic stem cell:	n/a	n/a
28	RUNX3	chr19:41194909-41195640	GM12878	blood:	n/a	n/a
29	RUNX3	chr19:41194996-41195723	GM12878	blood:	n/a	n/a
30	CBX3	chr19:41195112-41195574	K562	blood:	n/a	n/a
31	POLR2A	chr19:41194834-41197212	A549	lung:	n/a	n/a
32	POLR2A	chr19:41194391-41197325	HUVEC	blood vessel:	n/a	n/a
33	NFATC1	chr19:41194526-41195492	GM12878	blood:	n/a	n/a
34	POLR2A	chr19:41195227-41195654	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:41195237-41195659	GM12878	blood:	n/a	n/a
36	TCF3	chr19:41194988-41195332	GM12878	blood:	n/a	n/a
37	CHD1	chr19:41192595-41197591	IMR90	lung:	n/a	chr19:41196943-41196953 chr19:41196593-41196603
38	REST	chr19:41195043-41196885	H1-neurons	neurons:	n/a	chr19:41195235-41195253 chr19:41196100-41196120 chr19:41196105-41196114
39	POLR2A	chr19:41194936-41195322	MCF10A-Er-Src	breast:	n/a	n/a
40	GATA3	chr19:41195201-41197645	A549	lung:	n/a	n/a
41	STAT5A	chr19:41193198-41195366	GM12878	blood:	n/a	n/a
42	POLR2A	chr19:41195128-41195706	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr19:41195113-41197384	HUVEC	blood vessel:	n/a	n/a
44	BCL3	chr19:41194463-41195376	GM12878	blood:	n/a	n/a
45	NFATC1	chr19:41194152-41195486	GM12878	blood:	n/a	n/a
46	SP1	chr19:41194749-41197510	A549	lung:	n/a	chr19:41196322-41196334 chr19:41196565-41196574 chr19:41196982-41196993 chr19:41196563-41196575 chr19:41195450-41195464 chr19:41197386-41197398 chr19:41196296-41196310 chr19:41196606-41196615 chr19:41196594-41196603 chr19:41196601-41196622 chr19:41197386-41197398 chr19:41196564-41196573 chr19:41196604-41196616 chr19:41196894-41196904 chr19:41196604-41196616 chr19:41196983-41196992 chr19:41196595-41196604 chr19:41196564-41196574 chr19:41196942-41196951 chr19:41197267-41197276 chr19:41197271-41197280 chr19:41196605-41196614 chr19:41195697-41195711 chr19:41196941-41196952 chr19:41196605-41196614 chr19:41196322-41196334 chr19:41196594-41196603 chr19:41196563-41196575 chr19:41197267-41197281 chr19:41196982-41196994 chr19:41196605-41196615 chr19:41197387-41197401 chr19:41195752-41195762
47	SIN3AK20	chr19:41194961-41195545	SK-N-SH	brain:	n/a	n/a
48	PBX3	chr19:41195194-41197703	A549	lung:	n/a	chr19:41196611-41196620
49	POLR2A	chr19:41194963-41196330	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41193561..41199772-chr19:41221208..41225709,11	K562	blood:
2	chr19:41194676..41198444-chr19:41254531..41258137,9	MCF-7	breast:
3	chr19:41194976..41197680-chr19:41213933..41216402,2	MCF-7	breast:
4	chr19:41195260..41197933-chr19:41310864..41312582,2	K562	blood:
5	chr19:41193560..41201987-chr19:41206623..41212331,16	K562	blood:
6	chr19:41186952..41192144-chr19:41192156..41195982,8	MCF-7	breast:
7	chr19:41193720..41198590-chr19:41218677..41224410,19	MCF-7	breast:
8	chr19:41194805..41199772-chr19:41221674..41225965,11	K562	blood:
9	chr19:41195052..41198475-chr19:41206836..41210574,5	K562	blood:
10	chr19:41193182..41199089-chr19:41206241..41209564,9	MCF-7	breast:
11	chr19:41194241..41200533-chr19:41254244..41257966,10	K562	blood:
12	chr19:41194241..41198233-chr19:41254859..41260401,9	K562	blood:
13	chr19:41191453..41200740-chr19:41219595..41226457,20	MCF-7	breast:

Variant related genes	Relation type
NUMBL	TF binding region
ENSG00000123815	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000223284	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000105245	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10411347	0.81[GIH][hapmap]
rs2250994	0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap]
rs2561542	0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap]
rs2561543	0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap]
rs2561547	0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs2561551	0.80[ASN][1000 genomes]
rs2604860	0.85[GIH][hapmap]
rs2604892	0.81[JPT][hapmap]

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	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	nsv911723	chr19:41075990-41195279	Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv911727	chr19:41111069-41200511	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv911728	chr19:41111069-41211056	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv1058707	chr19:41146147-41200820	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv1067017	chr19:41185992-41231251	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
8	esv3432319	chr19:41190112-41196510	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
9	esv3391681	chr19:41192212-41196610	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
10	nsv820299	chr19:41193264-41195994	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41169800-41195400	Weak transcription	Psoas Muscle	Psoas
2	chr19:41175800-41196000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:41176200-41195600	Weak transcription	Small Intestine	intestine
4	chr19:41179200-41195800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr19:41179800-41196000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr19:41187000-41195600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:41187200-41195800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:41187600-41195800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr19:41188800-41195800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:41191800-41195600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:41192600-41195800	Weak transcription	Liver	Liver
12	chr19:41192600-41196000	Enhancers	Primary B cells from peripheral blood	blood
13	chr19:41192600-41196000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:41192800-41195600	Weak transcription	Thymus	Thymus
15	chr19:41193200-41195400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr19:41193400-41195400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:41193400-41195400	Enhancers	Gastric	stomach
18	chr19:41193400-41196200	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr19:41193400-41196200	Flanking Active TSS	K562	blood
20	chr19:41193600-41195400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:41193600-41195400	Flanking Active TSS	NHDF-Ad	bronchial
22	chr19:41193600-41195400	Flanking Active TSS	Osteobl	bone
23	chr19:41193600-41195600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:41193600-41195600	Flanking Active TSS	Fetal Brain Male	brain
25	chr19:41193600-41195600	Flanking Active TSS	NH-A	brain
26	chr19:41194000-41195600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr19:41194000-41195600	Flanking Active TSS	Rectal Smooth Muscle	rectum
28	chr19:41194000-41196200	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr19:41194000-41196200	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr19:41194000-41196800	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr19:41194200-41195800	Weak transcription	Stomach Mucosa	stomach
32	chr19:41194200-41196000	Flanking Active TSS	Fetal Stomach	stomach
33	chr19:41194200-41196800	Enhancers	Fetal Heart	heart
34	chr19:41194400-41197200	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr19:41194600-41195400	Flanking Active TSS	Fetal Lung	lung
36	chr19:41194600-41195600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:41194600-41195800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr19:41194600-41195800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:41194600-41196200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr19:41194600-41196200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr19:41194600-41196200	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr19:41194800-41195400	Flanking Active TSS	Fetal Kidney	kidney
43	chr19:41194800-41195400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr19:41194800-41195600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr19:41194800-41195600	Flanking Active TSS	Fetal Brain Female	brain
46	chr19:41194800-41195600	Enhancers	Fetal Thymus	thymus
47	chr19:41194800-41196000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:41194800-41196000	Enhancers	Primary T cells from cord blood	blood
49	chr19:41194800-41196000	Enhancers	Primary T cells fromperipheralblood	blood
50	chr19:41194800-41196200	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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