Variant report

Variant	rs541645181
Chromosome Location	chr2:99348402-99348403
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	chr2:99346578-99349177	HepG2	liver:	n/a	n/a
2	MAX	chr2:99346545-99348819	HepG2	liver:	n/a	chr2:99347002-99347012
3	CREB1	chr2:99346553-99348804	HepG2	liver:	n/a	n/a
4	PML	chr2:99347643-99348889	GM12878	blood:	n/a	n/a
5	REST	chr2:99347479-99348546	H1-neurons	neurons:	n/a	chr2:99347912-99347925 chr2:99347991-99348004 chr2:99348082-99348095 chr2:99347952-99347965
6	TEAD4	chr2:99348159-99349061	HepG2	liver:	n/a	n/a
7	RCOR1	chr2:99347694-99348703	HepG2	liver:	n/a	n/a
8	HEY1	chr2:99347663-99349341	HepG2	liver:	n/a	chr2:99348124-99348139 chr2:99348047-99348062
9	MYBL2	chr2:99347589-99348850	HepG2	liver:	n/a	n/a
10	NFIC	chr2:99348106-99348797	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:99347708-99349152	HepG2	liver:	n/a	n/a
12	TBP	chr2:99347675-99348707	HepG2	liver:	n/a	n/a
13	EP300	chr2:99347755-99348723	HepG2	liver:	n/a	chr2:99347861-99347877 chr2:99347844-99347860 chr2:99347866-99347882
14	TCF7L2	chr2:99347808-99348495	HEK293	kidney:	n/a	chr2:99348328-99348344 chr2:99348331-99348340 chr2:99348333-99348340 chr2:99348330-99348340 chr2:99348329-99348343
15	MXI1	chr2:99347485-99348809	SK-N-SH	brain:	n/a	n/a
16	MAX	chr2:99347631-99349230	HepG2	liver:	n/a	n/a
17	HEY1	chr2:99346496-99349205	HepG2	liver:	n/a	chr2:99347342-99347357 chr2:99347044-99347059 chr2:99347015-99347030 chr2:99348124-99348139 chr2:99348047-99348062
18	RUNX3	chr2:99348058-99348513	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:99347674-99348539	GM12892	blood:	n/a	n/a
20	POLR2A	chr2:99348102-99348770	HepG2	liver:	n/a	n/a
21	MYC	chr2:99347715-99348411	NB4	blood:	n/a	n/a
22	MYBL2	chr2:99348012-99348850	HepG2	liver:	n/a	n/a
23	POLR2A	chr2:99347636-99348842	HUVEC	blood vessel:	n/a	n/a
24	CEBPB	chr2:99348249-99348809	HepG2	liver:	n/a	n/a
25	NR2F2	chr2:99347439-99349190	HepG2	liver:	n/a	n/a
26	POLR2A	chr2:99347538-99348790	HUVEC	blood vessel:	n/a	n/a
27	EP300	chr2:99348080-99348854	HepG2	liver:	n/a	n/a
28	MAX	chr2:99347719-99348551	NB4	blood:	n/a	n/a
29	ARID3A	chr2:99348284-99349093	HepG2	liver:	n/a	n/a
30	POLR2A	chr2:99347659-99348654	HL-60	blood:	n/a	n/a
31	POLR2A	chr2:99347399-99348755	HepG2	liver:	n/a	n/a
32	MTA3	chr2:99347973-99348575	GM12878	blood:	n/a	n/a
33	POLR2A	chr2:99348080-99348648	GM12892	blood:	n/a	n/a
34	SIN3A	chr2:99347738-99348411	H1-hESC	embryonic stem cell:	n/a	chr2:99347912-99347925 chr2:99348095-99348108 chr2:99348082-99348095 chr2:99347988-99348001
35	POLR2A	chr2:99348038-99349260	HepG2	liver:	n/a	n/a
36	NFIC	chr2:99348124-99348805	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:99347509-99348787	GM12892	blood:	n/a	n/a
38	TCF7L2	chr2:99348186-99348508	PANC-1	pancreas:	n/a	chr2:99348328-99348344 chr2:99348331-99348340 chr2:99348333-99348340 chr2:99348330-99348340 chr2:99348329-99348343
39	NR2F2	chr2:99348122-99348902	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:99343338..99345259-chr2:99346373..99348700,3	MCF-7	breast:
2	chr2:99342514..99344879-chr2:99346177..99348798,2	K562	blood:
3	chr2:99344922..99348721-chr2:99382903..99389092,6	MCF-7	breast:
4	chr2:99348346..99350092-chr2:99446085..99447956,2	MCF-7	breast:
5	chr2:99342228..99344879-chr2:99346177..99348874,2	K562	blood:
6	chr2:99336480..99339286-chr2:99347871..99349769,2	MCF-7	breast:
7	chr2:99345368..99349321-chr2:99385005..99390572,6	MCF-7	breast:

Variant related genes	Relation type
MGAT4A	TF binding region
ENSG00000071073	Chromatin interaction
ENSG00000226791	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv535836	chr2:99329084-99353519	Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv535837	chr2:99329084-99358356	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv535838	chr2:99335416-99358356	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3377346	chr2:99345945-99348493	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv3405477	chr2:99346570-99349018	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3338485	chr2:99347070-99348418	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99344600-99348600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:99344800-99348600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
3	chr2:99345000-99348800	Active TSS	Duodenum Mucosa	Duodenum
4	chr2:99345600-99349200	Active TSS	Colonic Mucosa	Colon
5	chr2:99345800-99348600	Active TSS	Right Atrium	heart
6	chr2:99345800-99348800	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr2:99345800-99348800	Active TSS	Fetal Intestine Small	intestine
8	chr2:99345800-99348800	Active TSS	Right Ventricle	heart
9	chr2:99345800-99349400	Active TSS	Pancreas	Pancrea
10	chr2:99346000-99348600	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr2:99346000-99348600	Bivalent/Poised TSS	HepG2	liver
12	chr2:99346200-99348600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:99346200-99348600	Active TSS	Aorta	Aorta
14	chr2:99346200-99348800	Active TSS	Left Ventricle	heart
15	chr2:99346200-99348800	Active TSS	Lung	lung
16	chr2:99346200-99348800	Active TSS	Thymus	Thymus
17	chr2:99346400-99348600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr2:99346400-99348600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
19	chr2:99346600-99348600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:99346800-99348600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
21	chr2:99346800-99348600	Active TSS	Colon Smooth Muscle	Colon
22	chr2:99347000-99348600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:99347800-99348600	Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr2:99347800-99348600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:99347800-99348800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr2:99347800-99348800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:99348000-99348600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:99348000-99348600	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr2:99348000-99348600	Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr2:99348000-99348600	Flanking Active TSS	Liver	Liver
31	chr2:99348000-99348600	Active TSS	Fetal Kidney	kidney
32	chr2:99348000-99348600	Flanking Active TSS	HMEC	breast
33	chr2:99348000-99348800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr2:99348000-99348800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr2:99348000-99348800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:99348000-99348800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr2:99348000-99348800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr2:99348000-99349000	Flanking Active TSS	HUVEC	blood vessel
39	chr2:99348000-99349200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:99348000-99349400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr2:99348200-99348600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:99348200-99348600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
43	chr2:99348200-99348600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
44	chr2:99348200-99348600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
45	chr2:99348200-99348600	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:99348200-99348600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr2:99348200-99348600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:99348200-99348600	Bivalent/Poised TSS	Fetal Brain Female	brain
49	chr2:99348200-99348600	Flanking Active TSS	Fetal Heart	heart
50	chr2:99348200-99348600	Flanking Active TSS	A549	lung

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