Variant report

Variant	rs55913300
Chromosome Location	chr4:99181048-99181049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:99180313-99182895	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr4:99180509-99182731	K562	blood:	n/a	n/a
3	POLR2A	chr4:99180576-99183393	K562	blood:	n/a	n/a
4	POLR2A	chr4:99180639-99183583	Raji	blood:	n/a	n/a
5	POLR2A	chr4:99180532-99183540	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr4:99180609-99182928	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:99180827-99183493	GM18505	blood:	n/a	n/a
8	POLR2A	chr4:99180574-99182916	HepG2	liver:	n/a	n/a
9	POLR2A	chr4:99180520-99182433	HepG2	liver:	n/a	n/a
10	MXI1	chr4:99180419-99184597	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr4:99180518-99183485	GM12891	blood:	n/a	n/a
12	REST	chr4:99181015-99183708	H1-neurons	neurons:	n/a	chr4:99181845-99181865 chr4:99181848-99181861 chr4:99181845-99181865 chr4:99182563-99182581
13	POLR2A	chr4:99180632-99182421	HepG2	liver:	n/a	n/a
14	POLR2A	chr4:99180514-99183472	H1-hESC	embryonic stem cell:	n/a	n/a
15	MXI1	chr4:99180977-99184230	IMR90	lung:	n/a	n/a
16	POLR2A	chr4:99180989-99182777	HCT-116	colon:	n/a	n/a
17	POLR2A	chr4:99180750-99183508	K562	blood:	n/a	n/a
18	POLR2A	chr4:99180750-99182769	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:99180251-99183139	HepG2	liver:	n/a	n/a
20	POLR2A	chr4:99180500-99182965	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr4:99180655-99183623	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr4:99180686-99181098	SK-N-SH	brain:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:99063087..99065504-chr4:99179455..99182247,2	MCF-7	breast:
2	chr4:99086672..99088660-chr4:99180652..99182426,2	MCF-7	breast:
3	chr4:99180773..99182396-chr4:99197532..99199081,2	K562	blood:
4	chr4:99180005..99182414-chr4:99204613..99206874,2	K562	blood:
5	chr4:99166826..99169265-chr4:99180288..99182314,2	MCF-7	breast:
6	chr4:99062262..99068404-chr4:99178848..99183768,9	MCF-7	breast:
7	chr20:55837025..55838965-chr4:99178641..99181460,2	MCF-7	breast:
8	chr20:55925000..55927785-chr4:99180687..99182199,2	MCF-7	breast:
9	chr4:99177008..99180462-chr4:99180782..99182422,3	K562	blood:
10	chr4:99076051..99077551-chr4:99180191..99182364,2	MCF-7	breast:
11	chr4:99180743..99183219-chr4:99577927..99581407,3	MCF-7	breast:

No data

Variant related genes	Relation type
RAP1GDS1	TF binding region
ENSG00000168785	Chromatin interaction
ENSG00000260641	Chromatin interaction
ENSG00000163116	Chromatin interaction
ENSG00000101146	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs55634286	1.00[AMR][1000 genomes]
rs55699140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55942043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55950397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55987744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56022708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56030651	1.00[AMR][1000 genomes]
rs56032135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56038362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56075971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56081533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56110006	1.00[AMR][1000 genomes]
rs56128838	1.00[AMR][1000 genomes]
rs56199712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56262026	1.00[AMR][1000 genomes]
rs56743102	1.00[AMR][1000 genomes]
rs56813590	1.00[AMR][1000 genomes]
rs57012386	1.00[AMR][1000 genomes]
rs57375402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57678573	1.00[AMR][1000 genomes]
rs57911361	1.00[AMR][1000 genomes]
rs58507370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58579740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59399028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59643301	1.00[AMR][1000 genomes]
rs59911323	1.00[AMR][1000 genomes]
rs59980453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60107453	1.00[AMR][1000 genomes]
rs60148186	1.00[AMR][1000 genomes]
rs60218968	1.00[AMR][1000 genomes]
rs60460868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60467192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60473964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60502057	1.00[AMR][1000 genomes]
rs60551470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60883587	1.00[AMR][1000 genomes]
rs60969041	1.00[AMR][1000 genomes]
rs60998950	1.00[AMR][1000 genomes]
rs61537932	1.00[AMR][1000 genomes]
rs6814760	1.00[AMR][1000 genomes]
rs73832148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832175	1.00[AMR][1000 genomes]
rs73832177	1.00[AMR][1000 genomes]
rs73832178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832185	1.00[AMR][1000 genomes]
rs73832186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832190	1.00[AMR][1000 genomes]
rs73832194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73832303	1.00[AMR][1000 genomes]
rs73832304	1.00[AMR][1000 genomes]
rs73832310	1.00[AMR][1000 genomes]
rs73832312	1.00[AMR][1000 genomes]
rs73832313	1.00[AMR][1000 genomes]
rs73832314	1.00[AMR][1000 genomes]
rs73832315	1.00[AMR][1000 genomes]
rs73834405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834415	1.00[AMR][1000 genomes]
rs73834418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834420	1.00[AMR][1000 genomes]
rs73834421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73834430	1.00[AMR][1000 genomes]
rs73834432	1.00[AMR][1000 genomes]
rs73834433	1.00[AMR][1000 genomes]
rs73834440	1.00[AMR][1000 genomes]
rs73834441	1.00[AMR][1000 genomes]
rs73834442	1.00[AMR][1000 genomes]
rs73834446	1.00[AMR][1000 genomes]
rs73834447	1.00[AMR][1000 genomes]
rs73834448	1.00[AMR][1000 genomes]
rs73834449	1.00[AMR][1000 genomes]
rs73834450	1.00[AMR][1000 genomes]
rs73834451	1.00[AMR][1000 genomes]
rs73834457	1.00[AMR][1000 genomes]
rs73834458	1.00[AMR][1000 genomes]
rs73834459	1.00[AMR][1000 genomes]
rs73834460	1.00[AMR][1000 genomes]
rs73834462	1.00[AMR][1000 genomes]
rs73834463	1.00[AMR][1000 genomes]
rs73834464	1.00[AMR][1000 genomes]
rs73834465	1.00[AMR][1000 genomes]
rs73834469	1.00[AMR][1000 genomes]
rs73834472	1.00[AMR][1000 genomes]
rs73834473	1.00[AMR][1000 genomes]
rs73834477	1.00[AMR][1000 genomes]
rs73834483	1.00[AMR][1000 genomes]
rs73834484	1.00[AMR][1000 genomes]
rs73834486	1.00[AMR][1000 genomes]
rs73834488	1.00[AMR][1000 genomes]
rs73834491	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv1001570	chr4:98976239-99239838	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1004616	chr4:99085875-99308901	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv879652	chr4:99125659-99303633	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv528127	chr4:99146436-99229839	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv879653	chr4:99152631-99260423	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99180400-99181200	Enhancers	Primary T cells fromperipheralblood	blood
2	chr4:99180400-99181200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:99180400-99181200	Enhancers	Left Ventricle	heart
4	chr4:99180400-99181200	Enhancers	Sigmoid Colon	Sigmoid Colon
5	chr4:99180600-99181200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:99180600-99181200	Enhancers	H9 Cell Line	embryonic stem cell
7	chr4:99180600-99181200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr4:99180600-99181200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr4:99180600-99181200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:99180600-99181200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:99180600-99181200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:99180600-99181200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr4:99180600-99181200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:99180600-99181200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr4:99180600-99181200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:99180600-99181200	Flanking Active TSS	Brain Angular Gyrus	brain
17	chr4:99180600-99181200	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr4:99180600-99181200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:99180600-99181200	Flanking Active TSS	Colon Smooth Muscle	Colon
20	chr4:99180600-99181200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr4:99180600-99181200	Enhancers	Placenta	Placenta
22	chr4:99180600-99181200	Enhancers	Gastric	stomach
23	chr4:99180600-99181200	Enhancers	Pancreas	Pancrea
24	chr4:99180600-99181200	Enhancers	Placenta Amnion	Placenta Amnion
25	chr4:99180600-99181200	Enhancers	Psoas Muscle	Psoas
26	chr4:99180600-99181200	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr4:99180600-99181200	Flanking Active TSS	Dnd41	blood
28	chr4:99180600-99181200	Flanking Active TSS	NH-A	brain
29	chr4:99180600-99181400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr4:99180600-99181400	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr4:99180600-99181400	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr4:99180600-99181400	Flanking Active TSS	Fetal Heart	heart
33	chr4:99180600-99181400	Flanking Active TSS	Fetal Kidney	kidney
34	chr4:99180600-99181400	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr4:99180600-99181600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr4:99180600-99181600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:99180600-99181600	Flanking Active TSS	HMEC	breast
38	chr4:99180600-99181600	Flanking Active TSS	NHLF	lung
39	chr4:99180600-99181600	Flanking Active TSS	Osteobl	bone
40	chr4:99180600-99181800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:99180600-99181800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:99180600-99181800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr4:99180600-99182000	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr4:99180600-99182000	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr4:99180600-99182200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr4:99180600-99184000	Active TSS	HUES64 Cell Line	embryonic stem cell
47	chr4:99180800-99181200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:99180800-99181200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:99180800-99181200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr4:99180800-99181200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links