Variant report

Variant	rs72823599
Chromosome Location	chr17:46132424-46132425
allele	C/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	NRF1	chr17:46131588-46132711	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr17:46130865-46133815	K562	blood:	n/a	n/a
3	POLR2A	chr17:46132320-46133827	U87	brain:	n/a	n/a
4	POLR2A	chr17:46132336-46132695	HepG2	liver:	n/a	n/a
5	POLR2A	chr17:46130725-46133758	H1-hESC	embryonic stem cell:	n/a	n/a
6	RFX5	chr17:46130529-46133642	SK-N-SH	brain:	n/a	chr17:46130903-46130918
7	POLR2A	chr17:46132401-46133894	HCT-116	colon:	n/a	n/a
8	POLR2A	chr17:46130712-46133827	U87	brain:	n/a	n/a
9	POLR2A	chr17:46130712-46133948	U87	brain:	n/a	n/a
10	HMGN3	chr17:46132180-46132483	K562	blood:	n/a	n/a
11	SIN3A	chr17:46130822-46133793	H1-hESC	embryonic stem cell:	n/a	chr17:46132141-46132152
12	POLR2A	chr17:46132223-46132579	K562	blood:	n/a	n/a
13	POLR2A	chr17:46132222-46132538	HepG2	liver:	n/a	n/a
14	MXI1	chr17:46128980-46133584	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr17:46131122-46132543	K562	blood:	n/a	n/a
16	POLR2A	chr17:46131523-46133896	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr17:46132329-46133825	GM12878	blood:	n/a	n/a
18	SIN3AK20	chr17:46131161-46132490	H1-hESC	embryonic stem cell:	n/a	n/a
19	MTA3	chr17:46132323-46134396	GM12878	blood:	n/a	n/a
20	POLR2A	chr17:46132324-46132491	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr17:46131500-46132552	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr17:46132266-46133595	GM12878	blood:	n/a	n/a
23	POLR2A	chr17:46132421-46134257	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46033378..46035935-chr17:46129952..46132940,2	MCF-7	breast:

Variant related genes	Relation type
NFE2L1	TF binding region
ENSG00000167183	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10514938	1.00[ASN][1000 genomes]
rs11650615	1.00[ASN][1000 genomes]
rs16952265	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16953235	1.00[ASN][1000 genomes]
rs16953382	1.00[ASN][1000 genomes]
rs16953461	1.00[ASN][1000 genomes]
rs16953925	1.00[ASN][1000 genomes]
rs16954078	1.00[ASN][1000 genomes]
rs16954204	1.00[ASN][1000 genomes]
rs41280120	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41336845	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7216504	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823509	0.81[AMR][1000 genomes]
rs72823527	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823530	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823534	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823591	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72823592	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72823594	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72823601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825512	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825517	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825548	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72825584	1.00[ASN][1000 genomes]
rs8067005	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8073371	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 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	chr17:46127600-46132800	Genic enhancers	Fetal Intestine Small	intestine
2	chr17:46127800-46132600	Genic enhancers	Fetal Thymus	thymus
3	chr17:46127800-46133000	Genic enhancers	Fetal Intestine Large	intestine
4	chr17:46127800-46133200	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr17:46127800-46133200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
6	chr17:46127800-46133200	Genic enhancers	Placenta	Placenta
7	chr17:46127800-46133200	Genic enhancers	Pancreas	Pancrea
8	chr17:46127800-46133400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:46127800-46133600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr17:46128000-46132600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr17:46128000-46132600	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
12	chr17:46128000-46133000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
13	chr17:46128000-46133200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr17:46128000-46133800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr17:46128000-46134000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr17:46128000-46134000	Genic enhancers	Gastric	stomach
17	chr17:46128000-46134000	Genic enhancers	Monocytes-CD14+_RO01746	blood
18	chr17:46128000-46134400	Genic enhancers	Primary B cells from peripheral blood	blood
19	chr17:46128000-46138000	Genic enhancers	Spleen	Spleen
20	chr17:46128200-46132600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
21	chr17:46128200-46133400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr17:46128200-46133400	Genic enhancers	Lung	lung
23	chr17:46128200-46140800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr17:46128400-46132600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr17:46129800-46133200	Enhancers	Fetal Brain Male	brain
26	chr17:46129800-46133200	Enhancers	NHDF-Ad	bronchial
27	chr17:46129800-46134000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr17:46130200-46132800	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr17:46130200-46133400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr17:46130200-46133400	Genic enhancers	Dnd41	blood
31	chr17:46130200-46134000	Genic enhancers	K562	blood
32	chr17:46130400-46132600	Weak transcription	Primary B cells from cord blood	blood
33	chr17:46130400-46132600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr17:46130400-46132600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr17:46130400-46132800	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr17:46130400-46154600	Strong transcription	Primary T cells from cord blood	blood
37	chr17:46130600-46132800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr17:46130600-46133600	Genic enhancers	A549	lung
39	chr17:46130600-46149800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr17:46131000-46132600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr17:46131000-46132600	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr17:46131000-46132600	Flanking Active TSS	HMEC	breast
43	chr17:46131000-46133200	Weak transcription	Aorta	Aorta
44	chr17:46131000-46134600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr17:46131000-46145000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr17:46131200-46132800	Genic enhancers	Duodenum Mucosa	Duodenum
47	chr17:46131200-46133000	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr17:46131200-46133000	Genic enhancers	Rectal Mucosa Donor 31	rectum
49	chr17:46131200-46133200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr17:46131200-46133400	Genic enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links