Variant report

Variant	rs6815620
Chromosome Location	chr4:148864508-148864509
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	SPI1	chr4:148864230-148864608	GM12878	blood:	n/a	n/a
2	NFATC1	chr4:148864140-148864881	GM12878	blood:	n/a	n/a
3	STAT5A	chr4:148864172-148864686	GM12878	blood:	n/a	n/a
4	MTA3	chr4:148864107-148864953	GM12878	blood:	n/a	n/a
5	IKZF1	chr4:148864000-148864692	GM12878	blood:	n/a	n/a
6	ATF2	chr4:148864088-148864910	GM12878	blood:	n/a	chr4:148864728-148864735
7	IRF4	chr4:148864232-148864733	GM12878	blood:	n/a	chr4:148864698-148864712
8	NFATC1	chr4:148864122-148864642	GM12878	blood:	n/a	n/a
9	RUNX3	chr4:148863947-148865015	GM12878	blood:	n/a	n/a
10	FOXM1	chr4:148864135-148864859	GM12878	blood:	n/a	n/a
11	SPI1	chr4:148864360-148864535	GM12878	blood:	n/a	n/a
12	BATF	chr4:148864272-148864651	GM12878	blood:	n/a	n/a
13	TBL1XR1	chr4:148864114-148864865	GM12878	blood:	n/a	n/a
14	RFX5	chr4:148864338-148864718	GM12878	blood:	n/a	n/a
15	BCL11A	chr4:148864208-148864680	GM12878	blood:	n/a	n/a
16	PML	chr4:148863956-148864977	GM12878	blood:	n/a	n/a
17	MEF2C	chr4:148864128-148864707	GM12878	blood:	n/a	chr4:148864391-148864406
18	SP1	chr4:148864212-148864623	GM12878	blood:	n/a	n/a
19	NFIC	chr4:148863995-148864963	GM12878	blood:	n/a	n/a
20	NFIC	chr4:148864107-148864873	GM12878	blood:	n/a	n/a
21	CREB1	chr4:148864155-148864725	GM12878	blood:	n/a	n/a
22	SPI1	chr4:148864158-148864629	HL-60	blood:	n/a	n/a
23	IRF4	chr4:148864212-148864645	GM12878	blood:	n/a	n/a
24	CHD2	chr4:148864288-148864770	GM12878	blood:	n/a	n/a
25	BATF	chr4:148864246-148864664	GM12878	blood:	n/a	n/a
26	BHLHE40	chr4:148864181-148864947	GM12878	blood:	n/a	n/a
27	MEF2A	chr4:148864138-148864703	GM12878	blood:	n/a	chr4:148864391-148864406
28	EP300	chr4:148864119-148864856	GM12878	blood:	n/a	chr4:148864194-148864203 chr4:148864338-148864347 chr4:148864459-148864473
29	MEF2A	chr4:148864122-148864685	GM12878	blood:	n/a	chr4:148864391-148864406
30	SPI1	chr4:148864265-148864648	GM12891	blood:	n/a	n/a
31	RCOR1	chr4:148864111-148865001	GM12878	blood:	n/a	n/a
32	BCLAF1	chr4:148864138-148864663	GM12878	blood:	n/a	n/a
33	ZNF143	chr4:148864182-148864547	GM12878	blood:	n/a	n/a
34	STAT3	chr4:148864323-148864795	GM12878	blood:	n/a	n/a
35	BCL11A	chr4:148864303-148864562	GM12878	blood:	n/a	n/a
36	RUNX3	chr4:148864094-148864845	GM12878	blood:	n/a	n/a
37	NFYB	chr4:148864307-148864591	GM12878	blood:	n/a	n/a
38	EP300	chr4:148864029-148864857	GM12878	blood:	n/a	chr4:148864194-148864203 chr4:148864338-148864347 chr4:148864459-148864473 chr4:148864066-148864080
39	ATF2	chr4:148864139-148864803	GM12878	blood:	n/a	chr4:148864728-148864735
40	EBF1	chr4:148864137-148864797	GM12878	blood:	n/a	n/a
41	STAT5A	chr4:148864236-148864867	GM12878	blood:	n/a	n/a
42	EP300	chr4:148864210-148864837	GM12878	blood:	n/a	chr4:148864338-148864347 chr4:148864459-148864473
43	MXI1	chr4:148864207-148864849	GM12878	blood:	n/a	n/a
44	CREB1	chr4:148864192-148864940	GM12878	blood:	n/a	n/a
45	PAX5	chr4:148864247-148864764	GM12878	blood:	n/a	chr4:148864701-148864710
46	ZNF384	chr4:148864327-148864831	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:148603821..148605355-chr4:148862724..148865467,2	MCF-7	breast:

Variant related genes	Relation type
ARHGAP10	TF binding region
ENSG00000164169	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10010996	1.00[EUR][1000 genomes]
rs10012122	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10213616	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10519914	1.00[TSI][hapmap]
rs10519932	1.00[EUR][1000 genomes]
rs1436492	1.00[EUR][1000 genomes]
rs17023827	1.00[EUR][1000 genomes]
rs17023950	1.00[EUR][1000 genomes]
rs17023959	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17024108	1.00[EUR][1000 genomes]
rs17024163	1.00[EUR][1000 genomes]
rs17024360	1.00[TSI][hapmap]
rs17024397	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28371967	1.00[EUR][1000 genomes]
rs28647457	1.00[EUR][1000 genomes]
rs41435251	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4626180	0.81[AFR][1000 genomes]
rs5536	1.00[TSI][hapmap]
rs55689306	1.00[EUR][1000 genomes]
rs56742479	1.00[EUR][1000 genomes]
rs58776118	1.00[EUR][1000 genomes]
rs59129054	1.00[EUR][1000 genomes]
rs59222333	1.00[EUR][1000 genomes]
rs59845678	1.00[EUR][1000 genomes]
rs6813344	1.00[EUR][1000 genomes]
rs6848211	1.00[EUR][1000 genomes]
rs72957764	1.00[EUR][1000 genomes]
rs72957767	1.00[EUR][1000 genomes]
rs72957792	1.00[EUR][1000 genomes]
rs731989	1.00[EUR][1000 genomes]
rs73853711	1.00[EUR][1000 genomes]
rs7661589	1.00[EUR][1000 genomes]
rs7663257	1.00[EUR][1000 genomes]
rs7683313	1.00[TSI][hapmap]
rs7699281	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1017904	chr4:148814133-148975348	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1024596	chr4:148830472-148886915	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148796800-148866000	Weak transcription	Thymus	Thymus
2	chr4:148797400-148879600	Weak transcription	Gastric	stomach
3	chr4:148825400-148865800	Weak transcription	Fetal Lung	lung
4	chr4:148826600-148888200	Weak transcription	Fetal Thymus	thymus
5	chr4:148833600-148877400	Weak transcription	Small Intestine	intestine
6	chr4:148835000-148867200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:148835000-148869000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr4:148836600-148867000	Weak transcription	HMEC	breast
9	chr4:148847400-148877200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:148849200-148875600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr4:148850000-148876400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:148850200-148890800	Weak transcription	HUVEC	blood vessel
13	chr4:148854800-148866800	Weak transcription	NHEK	skin
14	chr4:148855200-148866000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:148855400-148868600	Weak transcription	Fetal Intestine Small	intestine
16	chr4:148855400-148884800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:148856400-148889000	Weak transcription	Placenta	Placenta
18	chr4:148859000-148867000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:148859400-148898000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr4:148859800-148878600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:148860600-148869400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:148860800-148879200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:148861800-148867000	Weak transcription	Fetal Stomach	stomach
24	chr4:148861800-148868600	Weak transcription	Right Ventricle	heart
25	chr4:148861800-148878400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:148861800-148883000	Weak transcription	Lung	lung
27	chr4:148861800-148883000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:148861800-148884800	Weak transcription	Esophagus	oesophagus
29	chr4:148861800-148885400	Weak transcription	Pancreas	Pancrea
30	chr4:148861800-148890800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr4:148862000-148865800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:148862000-148878400	Weak transcription	Fetal Heart	heart
33	chr4:148862000-148879200	Weak transcription	Psoas Muscle	Psoas
34	chr4:148862400-148865200	Weak transcription	Fetal Brain Male	brain
35	chr4:148862400-148867000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:148862600-148865800	Weak transcription	Fetal Muscle Leg	muscle
37	chr4:148862600-148866000	Weak transcription	Aorta	Aorta
38	chr4:148862600-148866000	Weak transcription	HSMMtube	muscle
39	chr4:148862600-148866800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:148862800-148865800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:148862800-148866000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr4:148862800-148867200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:148862800-148887800	Weak transcription	Fetal Intestine Large	intestine
44	chr4:148863400-148864600	Enhancers	Colon Smooth Muscle	Colon
45	chr4:148863600-148864600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:148863600-148864600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr4:148863600-148864600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:148863600-148864600	Enhancers	Muscle Satellite Cultured Cells	--
49	chr4:148863600-148865600	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr4:148863600-148865800	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links