Variant report

Variant	rs16846483
Chromosome Location	chr1:173834580-173834581
allele	A/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	chr1:173830742-173838152	GM18951	blood:	n/a	n/a
2	POLR2A	chr1:173834360-173838079	U87	brain:	n/a	n/a
3	POLR2A	chr1:173828332-173838242	K562	blood:	n/a	n/a
4	ATF2	chr1:173834423-173837701	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:173834558-173837359	U87	brain:	n/a	n/a
6	POLR2A	chr1:173825088-173838434	K562	blood:	n/a	n/a
7	POLR2A	chr1:173827997-173836225	HepG2	liver:	n/a	n/a
8	HEY1	chr1:173834548-173838164	K562	blood:	n/a	chr1:173837168-173837177 chr1:173837831-173837846 chr1:173837170-173837179
9	HEY1	chr1:173834529-173838121	K562	blood:	n/a	chr1:173837168-173837177 chr1:173837831-173837846 chr1:173837170-173837179
10	POLR2A	chr1:173824570-173837689	A549	lung:	n/a	n/a
11	POLR2A	chr1:173829284-173838362	K562	blood:	n/a	n/a
12	POLR2A	chr1:173829132-173838052	PFSK-1	brain:	n/a	n/a
13	CHD1	chr1:173831798-173837941	IMR90	lung:	n/a	chr1:173836993-173837000 chr1:173837608-173837618 chr1:173837832-173837842
14	POLR2A	chr1:173834511-173838174	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:173829663-173838350	K562	blood:	n/a	n/a
16	POLR2A	chr1:173829737-173838261	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr1:173834452-173838179	HL-60	blood:	n/a	n/a
18	POLR2A	chr1:173829767-173838193	GM12878	blood:	n/a	n/a
19	HEY1	chr1:173834488-173835484	HepG2	liver:	n/a	n/a
20	HEY1	chr1:173834492-173835968	HepG2	liver:	n/a	n/a
21	HCFC1	chr1:173834547-173839270	Hela-S3	cervix:	n/a	n/a
22	JUN	chr1:173832403-173840952	K562	blood:	n/a	chr1:173837048-173837062 chr1:173840939-173840951 chr1:173837421-173837430 chr1:173837165-173837178 chr1:173837443-173837452 chr1:173833568-173833581 chr1:173837835-173837844 chr1:173840672-173840683 chr1:173837169-173837178
23	POLR2A	chr1:173829700-173838480	GM18505	blood:	n/a	n/a
24	POLR2A	chr1:173834554-173838099	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr1:173834530-173835579	K562	blood:	n/a	n/a
26	POLR2A	chr1:173830001-173838163	GM12892	blood:	n/a	n/a
27	POLR2A	chr1:173834514-173837754	GM12891	blood:	n/a	n/a
28	POLR2A	chr1:173829120-173838093	GM12892	blood:	n/a	n/a
29	POLR2A	chr1:173828322-173838150	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr1:173829750-173838166	K562	blood:	n/a	n/a
31	POLR2A	chr1:173829165-173838292	GM19099	blood:	n/a	n/a
32	POLR2A	chr1:173834360-173837899	U87	brain:	n/a	n/a
33	MXI1	chr1:173834502-173840026	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr1:173829841-173838018	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:173830743-173837769	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:173829350-173838204	MCF-7	breast:	n/a	n/a
37	MXI1	chr1:173834357-173838222	K562	blood:	n/a	n/a
38	POLR2A	chr1:173828141-173838409	PANC-1	pancreas:	n/a	n/a
39	IRF1	chr1:173834324-173836341	K562	blood:	n/a	n/a
40	POLR2A	chr1:173834445-173837747	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr1:173829248-173838155	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr1:173834547-173838259	K562	blood:	n/a	n/a
43	POLR2A	chr1:173834495-173837799	SK-N-MC	brain:	n/a	n/a
44	POLR2A	chr1:173828033-173838432	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr1:173834505-173835496	HepG2	liver:	n/a	n/a
46	POLR2A	chr1:173829145-173838211	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr1:173828415-173838818	GM12891	blood:	n/a	n/a
48	POLR2A	chr1:173834521-173835244	GM12891	blood:	n/a	n/a
49	POLR2A	chr1:173829797-173838237	PFSK-1	brain:	n/a	n/a
50	POLR2A	chr1:173830660-173838208	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:173831929..173834882-chr1:173882309..173883868,2	MCF-7	breast:
2	chr1:173442536..173447801-chr1:173833439..173838851,7	K562	blood:
3	chr1:173789792..173811494-chr1:173827886..173840273,103	K562	blood:
4	chr1:173833761..173839509-chr1:173990118..173994234,9	K562	blood:
5	chr1:173684233..173688038-chr1:173834072..173837696,4	K562	blood:
6	chr1:173684233..173685986-chr1:173834072..173838019,3	K562	blood:
7	chr1:173831314..173839948-chr1:173984831..173993131,14	MCF-7	breast:
8	chr1:173832421..173839801-chr1:173885332..173891780,9	MCF-7	breast:
9	chr1:173834428..173840700-chr1:173878764..173885322,14	MCF-7	breast:
10	chr1:173831906..173839548-chr1:173987374..173993282,15	MCF-7	breast:
11	chr1:173789473..173804179-chr1:173828884..173842109,95	K562	blood:
12	chr1:173445658..173447676-chr1:173831376..173834939,3	K562	blood:
13	chr1:173833863..173839457-chr1:173910408..173918981,14	MCF-7	breast:

Variant related genes	Relation type
GAS5	TF binding region
ZBTB37	TF binding region
ENSG00000252231	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000076321	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000117601	Chromatin interaction
ENSG00000135870	Chromatin interaction
ENSG00000117592	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000236535	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1322769	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16846397	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2227620	1.00[AMR][1000 genomes]
rs57006357	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57343517	1.00[AMR][1000 genomes]
rs58576036	1.00[AMR][1000 genomes]
rs58930477	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59355797	1.00[AMR][1000 genomes]
rs59846661	1.00[AMR][1000 genomes]
rs6667627	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6704413	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73025612	1.00[AMR][1000 genomes]
rs73025620	1.00[AMR][1000 genomes]
rs73027407	1.00[AMR][1000 genomes]
rs73027443	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73027460	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73027463	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73027464	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73027488	1.00[AMR][1000 genomes]
rs73035116	1.00[AMR][1000 genomes]
rs73035134	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73035139	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73037076	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73037083	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73037097	1.00[AMR][1000 genomes]
rs73041050	1.00[AMR][1000 genomes]
rs73041059	1.00[AMR][1000 genomes]
rs7519571	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7531236	1.00[AMR][1000 genomes]
rs7539992	1.00[AMR][1000 genomes]
rs7547873	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9726181	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 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	chr1:173795000-173834600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:173818600-173834800	Strong transcription	Fetal Muscle Leg	muscle
3	chr1:173818600-173834800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr1:173819400-173834800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:173819600-173835600	Strong transcription	Fetal Muscle Trunk	muscle
6	chr1:173822800-173834800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:173823000-173835000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:173824800-173834600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr1:173829400-173834600	Strong transcription	Brain Anterior Caudate	brain
10	chr1:173829600-173834600	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:173829600-173835600	Strong transcription	Stomach Smooth Muscle	stomach
12	chr1:173830800-173834800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:173830800-173835000	Strong transcription	Ovary	ovary
14	chr1:173830800-173835800	Strong transcription	Placenta	Placenta
15	chr1:173831000-173834600	Strong transcription	Fetal Lung	lung
16	chr1:173831000-173834800	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:173831000-173835000	Strong transcription	Lung	lung
18	chr1:173831000-173835200	Strong transcription	Colon Smooth Muscle	Colon
19	chr1:173831000-173836000	Strong transcription	Left Ventricle	heart
20	chr1:173831200-173834800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:173831600-173835000	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr1:173831600-173835200	Strong transcription	Brain Germinal Matrix	brain
23	chr1:173831800-173834600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:173831800-173834800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:173831800-173834800	Strong transcription	Colonic Mucosa	Colon
26	chr1:173831800-173835000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:173831800-173837000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
28	chr1:173832000-173834800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:173832000-173835200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:173832200-173834800	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr1:173832200-173834800	Strong transcription	Rectal Smooth Muscle	rectum
32	chr1:173832200-173837000	Transcr. at gene 5' and 3'	K562	blood
33	chr1:173832400-173834800	Strong transcription	Brain Angular Gyrus	brain
34	chr1:173832400-173834800	Weak transcription	Esophagus	oesophagus
35	chr1:173832400-173836000	Weak transcription	Aorta	Aorta
36	chr1:173832400-173836600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
37	chr1:173832400-173837000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
38	chr1:173832600-173834600	Strong transcription	Brain Cingulate Gyrus	brain
39	chr1:173832600-173834600	Strong transcription	Fetal Kidney	kidney
40	chr1:173832600-173834800	Genic enhancers	Adipose Nuclei	Adipose
41	chr1:173832600-173835800	Weak transcription	Gastric	stomach
42	chr1:173832600-173836400	Transcr. at gene 5' and 3'	NH-A	brain
43	chr1:173832800-173835200	Strong transcription	Brain Substantia Nigra	brain
44	chr1:173832800-173835800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
45	chr1:173832800-173836400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:173832800-173836600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
47	chr1:173832800-173837000	Transcr. at gene 5' and 3'	A549	lung
48	chr1:173833000-173834600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:173833000-173836200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
50	chr1:173833000-173836400	Transcr. at gene 5' and 3'	NHLF	lung

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