Variant report

Variant	rs4241591
Chromosome Location	chr4:77121346-77121347
allele	A/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	TBL1XR1	chr4:77120741-77121499	GM12878	blood:	n/a	n/a
2	CHD2	chr4:77120724-77121358	GM12878	blood:	n/a	chr4:77121265-77121272
3	MTA3	chr4:77120553-77121489	GM12878	blood:	n/a	n/a
4	RUNX3	chr4:77120690-77121401	GM12878	blood:	n/a	n/a
5	PML	chr4:77120600-77121371	GM12878	blood:	n/a	n/a
6	USF2	chr4:77121328-77121663	GM12878	blood:	n/a	n/a
7	POU2F2	chr4:77120720-77121366	GM12891	blood:	n/a	chr4:77121006-77121014 chr4:77121003-77121018 chr4:77121001-77121019 chr4:77121004-77121015 chr4:77121005-77121015
8	ATF2	chr4:77120499-77121437	GM12878	blood:	n/a	n/a
9	EP300	chr4:77119136-77121422	GM12878	blood:	n/a	chr4:77120044-77120058
10	EBF1	chr4:77120649-77121412	GM12878	blood:	n/a	n/a
11	EBF1	chr4:77120627-77121540	GM12878	blood:	n/a	n/a
12	BHLHE40	chr4:77120674-77121459	GM12878	blood:	n/a	n/a
13	BCLAF1	chr4:77120532-77121349	GM12878	blood:	n/a	n/a
14	PAX5	chr4:77120586-77121437	GM12878	blood:	n/a	n/a
15	MEF2A	chr4:77120565-77121357	GM12878	blood:	n/a	n/a
16	CTCF	chr4:77121260-77121410	GM12864	blood:	n/a	n/a
17	RUNX3	chr4:77120613-77121402	GM12878	blood:	n/a	n/a
18	POU2F2	chr4:77120721-77121379	GM12878	blood:	n/a	chr4:77121006-77121014 chr4:77121003-77121018 chr4:77121001-77121019 chr4:77121004-77121015 chr4:77121005-77121015
19	IKZF1	chr4:77120653-77121513	GM12878	blood:	n/a	chr4:77121301-77121313
20	MTA3	chr4:77120623-77121347	GM12878	blood:	n/a	n/a
21	EP300	chr4:77120639-77121346	GM12878	blood:	n/a	n/a
22	STAT5A	chr4:77120519-77121485	GM12878	blood:	n/a	chr4:77120885-77120896
23	CTCF	chr4:77121200-77121350	GM12874	blood:	n/a	n/a
24	NFIC	chr4:77120563-77121460	GM12878	blood:	n/a	n/a
25	CTCF	chr4:77121220-77121370	GM12875	blood:	n/a	n/a
26	RELA	chr4:77120648-77121488	GM10847	blood:	n/a	n/a
27	RELA	chr4:77120766-77121460	GM18951	blood:	n/a	n/a
28	FOXM1	chr4:77118999-77121516	GM12878	blood:	n/a	n/a
29	NFIC	chr4:77118950-77121515	GM12878	blood:	n/a	chr4:77119704-77119721 chr4:77119704-77119720
30	WRNIP1	chr4:77120851-77121451	GM12878	blood:	n/a	n/a
31	RELA	chr4:77120706-77121355	GM19193	blood:	n/a	n/a
32	CTCF	chr4:77121205-77121356	GM12892	blood:	n/a	n/a
33	SPI1	chr4:77120531-77121384	GM12878	blood:	n/a	n/a
34	RELA	chr4:77120662-77121386	GM19099	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:77118780..77124053-chr4:77134347..77137767,5	MCF-7	breast:
2	chr4:77118894..77122374-chr4:77129647..77132337,3	K562	blood:
3	chr4:77120877..77123601-chr4:77133534..77136298,3	MCF-7	breast:
4	chr4:77114541..77118897-chr4:77119397..77123368,6	K562	blood:
5	chr4:77118497..77121388-chr4:77227077..77230082,4	MCF-7	breast:
6	chr4:77119760..77123050-chr4:77133589..77135332,3	K562	blood:

Variant related genes	Relation type
SCARB2	TF binding region
ENSG00000138760	Chromatin interaction
ENSG00000189157	Chromatin interaction
ENSG00000118804	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10017484	1.00[CHB][hapmap]
rs10022137	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10022519	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10030683	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11097232	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12331521	1.00[ASN][1000 genomes]
rs12508223	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13139234	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs17224545	1.00[JPT][hapmap]
rs4274876	0.92[ASN][1000 genomes]
rs4440243	1.00[ASN][1000 genomes]
rs4624679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4859613	0.92[ASN][1000 genomes]
rs4859619	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4859622	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6532181	0.92[ASN][1000 genomes]
rs6532230	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6814012	1.00[CHB][hapmap]
rs6814817	1.00[CHB][hapmap]
rs6824953	0.87[YRI][hapmap];0.92[AFR][1000 genomes]
rs6857166	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7654988	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7697711	1.00[CHB][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs894250	0.82[CEU][hapmap]
rs9990550	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9992976	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799666	chr4:77119942-77129568	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4241591	CCDC158	cis	parietal	SCAN
rs4241591	BTC	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77113200-77134000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:77113600-77134200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:77114200-77122400	Enhancers	Right Ventricle	heart
4	chr4:77114600-77122000	Enhancers	HMEC	breast
5	chr4:77114800-77122800	Enhancers	Psoas Muscle	Psoas
6	chr4:77115200-77122200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:77115400-77122600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:77116200-77122400	Enhancers	Pancreas	Pancrea
9	chr4:77116200-77122400	Enhancers	Right Atrium	heart
10	chr4:77116600-77122600	Enhancers	Fetal Thymus	thymus
11	chr4:77116800-77122200	Enhancers	Primary B cells from peripheral blood	blood
12	chr4:77117000-77122800	Enhancers	Small Intestine	intestine
13	chr4:77117000-77134000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:77117200-77121400	Enhancers	Spleen	Spleen
15	chr4:77117200-77129200	Enhancers	Liver	Liver
16	chr4:77117400-77122600	Enhancers	Thymus	Thymus
17	chr4:77117400-77132800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:77117800-77122200	Enhancers	NHDF-Ad	bronchial
19	chr4:77117800-77122400	Enhancers	Left Ventricle	heart
20	chr4:77117800-77122800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr4:77118000-77121400	Enhancers	Aorta	Aorta
22	chr4:77118000-77122000	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr4:77118000-77122400	Enhancers	Fetal Heart	heart
24	chr4:77118200-77121600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr4:77118200-77122600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr4:77118400-77121800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:77118400-77122000	Enhancers	Primary T cells from cord blood	blood
28	chr4:77118600-77121800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr4:77118600-77122400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr4:77118800-77121800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr4:77118800-77122000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr4:77118800-77122200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:77118800-77122400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr4:77118800-77122400	Enhancers	Fetal Stomach	stomach
35	chr4:77118800-77122600	Enhancers	Fetal Muscle Leg	muscle
36	chr4:77118800-77123000	Enhancers	Stomach Mucosa	stomach
37	chr4:77118800-77124200	Enhancers	Fetal Intestine Large	intestine
38	chr4:77118800-77125400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:77119000-77121400	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr4:77119000-77121400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:77119000-77121600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr4:77119000-77121600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:77119200-77121400	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr4:77119200-77121400	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr4:77119200-77121400	Enhancers	Primary T cells fromperipheralblood	blood
46	chr4:77119200-77121400	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr4:77119200-77121400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:77119200-77121600	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr4:77119200-77122000	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr4:77119200-77122000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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