Variant report

Variant	rs1858846
Chromosome Location	chr19:19281187-19281188
allele	G/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	NR2F2	chr19:19280935-19281581	MCF-7	breast:	n/a	n/a
2	ZBTB7A	chr19:19280916-19281701	K562	blood:	n/a	chr19:19281264-19281273
3	POLR2A	chr19:19280644-19281419	MCF-7	breast:	n/a	n/a
4	RCOR1	chr19:19280986-19281289	HepG2	liver:	n/a	n/a
5	BHLHE40	chr19:19280833-19281279	K562	blood:	n/a	chr19:19281075-19281091 chr19:19281047-19281063
6	POLR2A	chr19:19280750-19281467	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr19:19280663-19281408	GM19099	blood:	n/a	n/a
8	POLR2A	chr19:19280841-19281418	K562	blood:	n/a	n/a
9	TAF1	chr19:19280935-19281188	HepG2	liver:	n/a	n/a
10	POLR2A	chr19:19280410-19281227	GM12891	blood:	n/a	n/a
11	POLR2A	chr19:19280775-19281436	GM18526	blood:	n/a	n/a
12	MAX	chr19:19280871-19281282	K562	blood:	n/a	n/a
13	RELA	chr19:19280457-19281198	GM18951	blood:	n/a	n/a
14	POU2F2	chr19:19280741-19281371	GM12878	blood:	n/a	chr19:19281145-19281155 chr19:19281143-19281158 chr19:19281147-19281154 chr19:19281145-19281155 chr19:19281147-19281155 chr19:19281146-19281157 chr19:19281146-19281155 chr19:19281144-19281156 chr19:19281146-19281156 chr19:19281144-19281158 chr19:19281142-19281160
15	RXRA	chr19:19281095-19281475	H1-hESC	embryonic stem cell:	n/a	chr19:19281212-19281219
16	TCF3	chr19:19280825-19281311	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:19280588-19281429	GM19193	blood:	n/a	n/a
18	MAX	chr19:19280805-19281340	ECC-1	luminal epithelium:	n/a	chr19:19281294-19281304
19	HMGN3	chr19:19280849-19281620	K562	blood:	n/a	n/a
20	POLR2A	chr19:19280816-19281345	K562	blood:	n/a	n/a
21	NANOG	chr19:19280895-19281239	H1-hESC	embryonic stem cell:	n/a	chr19:19281147-19281156
22	POLR2A	chr19:19280379-19281352	GM12878	blood:	n/a	n/a
23	FOXP2	chr19:19281002-19281275	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr19:19280837-19281301	GM10847	blood:	n/a	n/a
25	MXI1	chr19:19280914-19281237	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:19280803-19281294	ECC-1	luminal epithelium:	n/a	n/a
27	MAX	chr19:19280802-19281316	ECC-1	luminal epithelium:	n/a	chr19:19281294-19281304
28	YY1	chr19:19280873-19281365	HepG2	liver:	n/a	chr19:19281078-19281092
29	POLR2A	chr19:19280371-19281543	GM12891	blood:	n/a	n/a
30	POLR2A	chr19:19280727-19281403	GM18951	blood:	n/a	n/a
31	POLR2A	chr19:19280472-19281641	HepG2	liver:	n/a	n/a
32	POLR2A	chr19:19280686-19281427	GM18505	blood:	n/a	n/a
33	POLR2A	chr19:19280686-19281582	GM15510	blood:	n/a	n/a
34	POLR2A	chr19:19280477-19281250	GM12878	blood:	n/a	n/a
35	HEY1	chr19:19280902-19281280	HepG2	liver:	n/a	n/a
36	BACH1	chr19:19281158-19281338	H1-hESC	embryonic stem cell:	n/a	n/a
37	POU2F2	chr19:19280884-19281258	GM12878	blood:	n/a	chr19:19281145-19281155 chr19:19281143-19281158 chr19:19281147-19281154 chr19:19281145-19281155 chr19:19281147-19281155 chr19:19281146-19281157 chr19:19281146-19281155 chr19:19281144-19281156 chr19:19281146-19281156 chr19:19281144-19281158 chr19:19281142-19281160
38	POLR2A	chr19:19280634-19281284	GM12891	blood:	n/a	n/a
39	POLR2A	chr19:19280871-19281392	MCF-7	breast:	n/a	n/a
40	STAT1	chr19:19280593-19281309	GM12878	blood:	n/a	n/a
41	MAZ	chr19:19280933-19281237	HepG2	liver:	n/a	n/a
42	SP1	chr19:19280919-19281511	H1-hESC	embryonic stem cell:	n/a	chr19:19281116-19281137 chr19:19281192-19281202 chr19:19281328-19281337 chr19:19281192-19281202 chr19:19281296-19281310
43	POLR2A	chr19:19280649-19281247	GM12892	blood:	n/a	n/a
44	MAX	chr19:19281013-19281232	HepG2	liver:	n/a	n/a
45	CHD2	chr19:19281097-19281403	H1-hESC	embryonic stem cell:	n/a	n/a
46	SP4	chr19:19280880-19281421	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr19:19280812-19281234	HepG2	liver:	n/a	n/a
48	POLR2A	chr19:19280893-19281349	HepG2	liver:	n/a	n/a
49	IRF1	chr19:19280964-19281421	K562	blood:	n/a	n/a
50	TBP	chr19:19280981-19281203	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:19281140-19281190	Jurkat	blood:	n/a
2	chr19:19281175-19281225	Caco-2	colon:	n/a
3	chr19:19281140-19281190	U87	brain:	n/a
4	chr19:19281140-19281190	PFSK-1	brain:	n/a
5	chr19:19281185-19281235	H1-hESC	embryonic stem cell:	embryo
6	chr19:19281140-19281190	SAEC	small airway:	n/a
7	chr19:19281185-19281235	HRE	kidney:	n/a
8	chr19:19281140-19281190	NHDF-neo	bronchial:	n/a
9	chr19:19281140-19281190	H1-hESC	embryonic stem cell:	embryo
10	chr19:19281185-19281235	SK-N-SH	brain:	n/a
11	chr19:19281175-19281225	PANC-1	pancreas:	n/a
12	chr19:19281185-19281235	HEEpiC	esophagus:	n/a
13	chr19:19281175-19281225	HAEpiC	amniotic membrane:	n/a
14	chr19:19281185-19281235	SK-N-SH_RA	brain:	n/a
15	chr19:19281175-19281225	PrEC	prostate:	n/a
16	chr19:19281185-19281235	HCF	heart:	n/a
17	chr19:19281185-19281235	NH-A	brain:	n/a
18	chr19:19281185-19281235	ECC-1	luminal epithelium:	n/a
19	chr19:19281140-19281190	ovcar-3	ovarian:	n/a
20	chr19:19281175-19281225	RPTEC	kidney:	n/a
21	chr19:19281185-19281235	BJ	skin:	n/a
22	chr19:19281185-19281235	AG09309	skin:	n/a
23	chr19:19281140-19281190	RPTEC	kidney:	n/a
24	chr19:19281175-19281225	ovcar-3	ovarian:	n/a
25	chr19:19281140-19281190	PrEC	prostate:	n/a
26	chr19:19281140-19281190	AoSMC	blood vessel:	n/a
27	chr19:19281185-19281235	PrEC	prostate:	n/a
28	chr19:19281175-19281225	HNPCEpiC	eye:	n/a
29	chr19:19281140-19281190	CMK	blood:	n/a
30	chr19:19281185-19281235	CMK	blood:	n/a
31	chr19:19281185-19281235	RPTEC	kidney:	n/a
32	chr19:19281175-19281225	GM12878	blood:	n/a
33	chr19:19281175-19281225	AG09309	skin:	n/a
34	chr19:19281175-19281225	AG04450	lung:	fetal
35	chr19:19281185-19281235	GM19239	blood:	n/a
36	chr19:19281175-19281225	ECC-1	luminal epithelium:	n/a
37	chr19:19281140-19281190	PANC-1	pancreas:	n/a
38	chr19:19281185-19281235	T-47D	breast:	n/a
39	chr19:19281140-19281190	SKMC	muscle:	n/a
40	chr19:19281185-19281235	SAEC	small airway:	n/a
41	chr19:19281140-19281190	LNCaP	prostate:	n/a
42	chr19:19281185-19281235	HIPEpiC	eye:	n/a
43	chr19:19281140-19281190	GM12891	blood:	n/a
44	chr19:19281140-19281190	K562	blood:	n/a
45	chr19:19281140-19281190	SK-N-MC	brain:	n/a
46	chr19:19281140-19281190	HCPEpiC	choroid plexus:	n/a
47	chr19:19281185-19281235	GM12891	blood:	n/a
48	chr19:19281185-19281235	HCPEpiC	choroid plexus:	n/a
49	chr19:19281140-19281190	GM06990	blood:	n/a
50	chr19:19281175-19281225	AG04449	skin:	fetal

No.	Distal block	Cell Line	Cell type
1	chr19:19280644..19282541-chr19:19431552..19433735,2	MCF-7	breast:
2	chr19:19280114..19282646-chr19:19429552..19431405,2	MCF-7	breast:
3	chr19:19279506..19282646-chr19:19302669..19304636,3	MCF-7	breast:
4	chr19:19276770..19279555-chr19:19281152..19284239,3	K562	blood:

Variant related genes	Relation type
MEF2B	TF binding region
MEF2B	CpG island
ENSG00000129933	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000105705	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000064489	Chromatin interaction
ENSG00000254901	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1005980	0.92[ASN][1000 genomes]
rs10417796	0.84[EUR][1000 genomes]
rs10418053	0.84[EUR][1000 genomes]
rs1050544	0.84[EUR][1000 genomes]
rs10854008	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10854009	0.83[EUR][1000 genomes]
rs10854012	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11669408	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11669860	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11669861	0.87[EUR][1000 genomes]
rs12609573	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12972894	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12974672	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12975096	0.80[EUR][1000 genomes]
rs12975253	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12975290	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12980269	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12980955	0.85[EUR][1000 genomes]
rs12981160	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238668	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239369	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2239370	0.83[EUR][1000 genomes]
rs2283623	0.85[EUR][1000 genomes]
rs2314035	0.84[EUR][1000 genomes]
rs35342977	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787040	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808185	0.82[EUR][1000 genomes]
rs539	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62135499	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71332145	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250650	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7256811	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260127	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72997174	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs741706	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101388	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19249600-19282600	Weak transcription	NHLF	lung
2	chr19:19259000-19290200	Weak transcription	Colon Smooth Muscle	Colon
3	chr19:19268200-19282600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr19:19268800-19287200	Weak transcription	Dnd41	blood
5	chr19:19277400-19300600	Weak transcription	Small Intestine	intestine
6	chr19:19280200-19281800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:19280200-19281800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr19:19280400-19281200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr19:19280400-19281200	Flanking Active TSS	GM12878-XiMat	blood
10	chr19:19280400-19281400	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr19:19280400-19281400	Enhancers	Gastric	stomach
12	chr19:19280400-19281400	Enhancers	Lung	lung
13	chr19:19280400-19281600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:19280400-19281600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr19:19280400-19281600	Bivalent Enhancer	Fetal Intestine Small	intestine
16	chr19:19280400-19281800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:19280400-19281800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:19280400-19281800	Enhancers	Stomach Mucosa	stomach
19	chr19:19280400-19281800	Flanking Active TSS	HepG2	liver
20	chr19:19280600-19281400	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr19:19280600-19281400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
22	chr19:19280600-19281400	Flanking Active TSS	K562	blood
23	chr19:19280600-19281600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
24	chr19:19280600-19281600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr19:19280600-19281600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr19:19280600-19281600	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr19:19280600-19281600	Enhancers	Primary hematopoietic stem cells	blood
28	chr19:19280600-19281600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr19:19280600-19281600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr19:19280600-19281600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr19:19280600-19281800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
32	chr19:19280600-19282000	Bivalent Enhancer	Fetal Stomach	stomach
33	chr19:19280800-19281200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:19280800-19281200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr19:19280800-19281200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr19:19280800-19281200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:19280800-19281200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr19:19280800-19281200	Active TSS	Muscle Satellite Cultured Cells	--
39	chr19:19280800-19281200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:19280800-19281200	Enhancers	Liver	Liver
41	chr19:19280800-19281200	Active TSS	Brain Anterior Caudate	brain
42	chr19:19280800-19281200	Active TSS	Brain Cingulate Gyrus	brain
43	chr19:19280800-19281200	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr19:19280800-19281200	Flanking Active TSS	Pancreas	Pancrea
45	chr19:19280800-19281200	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr19:19280800-19281200	Flanking Active TSS	Right Ventricle	heart
47	chr19:19280800-19281200	Flanking Active TSS	Thymus	Thymus
48	chr19:19280800-19281200	Flanking Active TSS	Spleen	Spleen
49	chr19:19280800-19281200	Active TSS	HSMM	muscle
50	chr19:19280800-19281400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

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