Variant report

Variant	rs546237576
Chromosome Location	chr19:55864983-55864984
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	MAX	chr19:55864700-55866015	K562	blood:	n/a	chr19:55865340-55865350
2	POLR2A	chr19:55864724-55865787	H1-neurons	neurons:	n/a	n/a
3	SP1	chr19:55864929-55865951	A549	lung:	n/a	chr19:55865382-55865394 chr19:55865428-55865439 chr19:55865383-55865392 chr19:55865362-55865372 chr19:55865428-55865440 chr19:55865339-55865351 chr19:55865157-55865171 chr19:55865458-55865469 chr19:55865382-55865394 chr19:55865362-55865372 chr19:55865429-55865443
4	SIN3A	chr19:55864703-55865882	H1-hESC	embryonic stem cell:	n/a	n/a
5	SP4	chr19:55864969-55865663	H1-hESC	embryonic stem cell:	n/a	chr19:55865380-55865396 chr19:55865428-55865439 chr19:55865428-55865444 chr19:55865359-55865375 chr19:55865458-55865469
6	TCF7L2	chr19:55864901-55865102	PANC-1	pancreas:	n/a	n/a
7	REST	chr19:55864914-55865174	A549	lung:	n/a	n/a
8	MAX	chr19:55864874-55865949	A549	lung:	n/a	chr19:55865340-55865350
9	E2F6	chr19:55864933-55865933	A549	lung:	n/a	chr19:55865340-55865349
10	MAX	chr19:55864965-55865824	A549	lung:	n/a	chr19:55865340-55865350
11	IRF1	chr19:55864964-55865882	K562	blood:	n/a	chr19:55865359-55865373 chr19:55865426-55865440 chr19:55865380-55865394
12	REST	chr19:55864565-55865603	H1-neurons	neurons:	n/a	chr19:55864674-55864682

No.	Distal block	Cell Line	Cell type
1	chr19:55864929..55868342-chr19:55869494..55871064,3	MCF-7	breast:
2	chr19:55725474..55728358-chr19:55864550..55866958,2	K562	blood:
3	chr19:55768392..55770990-chr19:55864103..55865699,2	MCF-7	breast:
4	chr19:55863699..55867009-chr19:55895864..55899065,4	MCF-7	breast:
5	chr19:55864955..55867658-chr19:55880222..55883231,3	MCF-7	breast:
6	chr19:55864065..55867080-chr19:55895058..55897568,4	K562	blood:
7	chr19:55864307..55867114-chr19:56165229..56167152,3	K562	blood:
8	chr19:55726786..55728358-chr19:55864550..55866363,2	K562	blood:
9	chr19:55862642..55868480-chr19:55895176..55899926,10	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM71E2-1	chr19:55864975-55865057	NONHSAT068026

Variant related genes	Relation type
COX6B2	TF binding region
ENSG00000063244	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000095752	Chromatin interaction
ENSG00000267706	Chromatin interaction
ENSG00000105063	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats 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	59 gene(s)	inside rSNPs	diseases
4	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
5	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
6	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
7	nsv912460	chr19:55814881-55897327	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
8	nsv912461	chr19:55845386-55897327	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Strong transcription Weak transcription 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	99 gene(s)	inside rSNPs	diseases
9	nsv470162	chr19:55845386-55902257	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
10	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
11	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
12	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer 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 miRNA target site	203 gene(s)	inside rSNPs	diseases
13	esv1799638	chr19:55850652-55883879	Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	nsv516199	chr19:55854313-55901099	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
15	nsv912465	chr19:55854313-55935184	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS 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 miRNA target site	196 gene(s)	inside rSNPs	diseases
16	esv3430654	chr19:55864590-55867488	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55863200-55865000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:55863200-55865000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
3	chr19:55863200-55865800	Bivalent Enhancer	Stomach Mucosa	stomach
4	chr19:55863600-55865000	Bivalent Enhancer	Fetal Intestine Large	intestine
5	chr19:55863600-55865000	Bivalent Enhancer	Fetal Intestine Small	intestine
6	chr19:55863800-55865200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr19:55864000-55865000	Bivalent Enhancer	Placenta	Placenta
8	chr19:55864000-55865400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:55864200-55865000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
10	chr19:55864400-55865000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:55864400-55865000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
12	chr19:55864400-55865000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
13	chr19:55864400-55865000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:55864400-55865000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
15	chr19:55864400-55865200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
16	chr19:55864400-55865200	Enhancers	Gastric	stomach
17	chr19:55864400-55866000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:55864400-55866000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:55864400-55866200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:55864600-55865000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr19:55864600-55865000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
22	chr19:55864600-55865000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
23	chr19:55864600-55865000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
24	chr19:55864600-55865000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
25	chr19:55864600-55865000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:55864600-55865000	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
27	chr19:55864600-55865000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:55864600-55865000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:55864600-55865000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
30	chr19:55864600-55865000	Bivalent Enhancer	Brain Angular Gyrus	brain
31	chr19:55864600-55865000	Bivalent Enhancer	Fetal Brain Male	brain
32	chr19:55864600-55865000	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr19:55864600-55865000	Enhancers	Pancreas	Pancrea
34	chr19:55864600-55865000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
35	chr19:55864600-55865200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
36	chr19:55864600-55865200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
37	chr19:55864600-55865200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr19:55864600-55865200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
39	chr19:55864600-55865200	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
40	chr19:55864600-55865200	Bivalent Enhancer	Fetal Thymus	thymus
41	chr19:55864600-55865200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
42	chr19:55864600-55865200	Bivalent Enhancer	Spleen	Spleen
43	chr19:55864600-55865400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
44	chr19:55864600-55865400	Flanking Bivalent TSS/Enh	Right Ventricle	heart
45	chr19:55864600-55865600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
46	chr19:55864600-55866000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr19:55864600-55866200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
48	chr19:55864600-55866200	Enhancers	Lung	lung
49	chr19:55864600-55866400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:55864800-55865000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell

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