Variant report

Variant	rs1426138
Chromosome Location	chr4:79701528-79701529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr4:79700977-79701585	K562	blood:	n/a	n/a
2	POLR2A	chr4:79695600-79704800	PBDE	blood:	n/a	n/a
3	GATA1	chr4:79701047-79701687	PBDE	blood:	n/a	chr4:79701129-79701140
4	JUND	chr4:79701234-79701555	K562	blood:	n/a	n/a
5	POLR2A	chr4:79699817-79701630	GM12878	blood:	n/a	n/a
6	RCOR1	chr4:79701248-79701579	K562	blood:	n/a	n/a
7	POLR2A	chr4:79699498-79704548	K562	blood:	n/a	n/a
8	MAZ	chr4:79701087-79701573	K562	blood:	n/a	n/a
9	CEBPD	chr4:79701184-79701688	K562	blood:	n/a	n/a
10	MYC	chr4:79701234-79701556	K562	blood:	n/a	n/a
11	EP300	chr4:79700936-79701632	K562	blood:	n/a	chr4:79701015-79701029
12	POLR2A	chr4:79701399-79701556	K562	blood:	n/a	n/a
13	HMGN3	chr4:79701276-79701554	K562	blood:	n/a	n/a
14	POLR2A	chr4:79701511-79701553	MCF10A-Er-Src	breast:	n/a	n/a
15	TEAD4	chr4:79699532-79701679	K562	blood:	n/a	n/a
16	TEAD4	chr4:79701026-79701597	K562	blood:	n/a	n/a
17	POLR2A	chr4:79699514-79703652	GM12891	blood:	n/a	n/a
18	POLR2A	chr4:79701112-79701680	K562	blood:	n/a	n/a
19	TBL1XR1	chr4:79698151-79701864	K562	blood:	n/a	n/a
20	POLR2A	chr4:79701172-79703417	K562	blood:	n/a	n/a
21	ZC3H11A	chr4:79701328-79701818	K562	blood:	n/a	n/a
22	MYC	chr4:79700519-79701628	K562	blood:	n/a	chr4:79700715-79700725
23	TBP	chr4:79701349-79701558	K562	blood:	n/a	n/a
24	IRF1	chr4:79700076-79701596	K562	blood:	n/a	n/a
25	PML	chr4:79699511-79703925	K562	blood:	n/a	n/a
26	ZMIZ1	chr4:79701038-79701549	K562	blood:	n/a	n/a
27	TAL1	chr4:79701263-79701595	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:79561055..79563429-chr4:79700959..79703090,2	K562	blood:
2	chr4:79700005..79702087-chr4:79782609..79785586,2	MCF-7	breast:
3	chr4:79699190..79702080-chr4:79704302..79706989,3	MCF-7	breast:
4	chr4:79593540..79596329-chr4:79699312..79702683,3	K562	blood:
5	chr4:79700579..79703463-chr4:79781034..79782674,2	MCF-7	breast:
6	chr4:79573461..79577118-chr4:79700688..79703892,3	K562	blood:
7	chr4:79547801..79550163-chr4:79699958..79704022,3	K562	blood:
8	chr4:79571366..79573433-chr4:79699664..79702069,2	K562	blood:
9	chr4:79610837..79614309-chr4:79701098..79703975,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260278	TF binding region
ENSG00000238816	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10028067	0.89[CHB][hapmap]
rs1061400	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs10857059	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs1299129	0.89[CHB][hapmap];0.86[CHD][hapmap];0.85[LWK][hapmap]
rs13122868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs13138005	1.00[YRI][hapmap]
rs13138117	0.89[CHB][hapmap]
rs1871706	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs7664587	0.89[CHB][hapmap];0.86[CHD][hapmap]
rs9307446	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1803379	chr4:79661618-79704210	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv1792021	chr4:79661618-79784245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
3	esv1792429	chr4:79697116-79704210	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv1798320	chr4:79697116-79704210	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv1801852	chr4:79697116-79704210	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv1802642	chr4:79697116-79704210	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv1802703	chr4:79697116-79704210	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv1833723	chr4:79697116-79704210	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	esv1833992	chr4:79697116-79704210	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv1835474	chr4:79697116-79704210	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	esv1837381	chr4:79697116-79704210	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	esv1845915	chr4:79697116-79704210	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1426138	LIN54	cis	cerebellum	SCAN
rs1426138	PRDM8	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79698600-79702200	Weak transcription	Gastric	stomach
2	chr4:79698600-79702200	Weak transcription	Spleen	Spleen
3	chr4:79698600-79703200	Weak transcription	Ovary	ovary
4	chr4:79698600-79708600	Weak transcription	Pancreas	Pancrea
5	chr4:79698800-79703200	Weak transcription	Stomach Mucosa	stomach
6	chr4:79698800-79705200	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:79699000-79701600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr4:79699000-79702000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:79699000-79702000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr4:79699000-79703000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:79699000-79717200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:79699200-79702000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr4:79699200-79704200	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr4:79699200-79704800	Weak transcription	Psoas Muscle	Psoas
15	chr4:79699200-79709000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:79699200-79709200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:79699400-79701800	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr4:79699400-79704200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr4:79699400-79722600	Weak transcription	Fetal Thymus	thymus
20	chr4:79699600-79701600	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr4:79699600-79705000	Weak transcription	NH-A	brain
22	chr4:79699800-79702000	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr4:79699800-79702000	Enhancers	Liver	Liver
24	chr4:79699800-79703000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:79700000-79704600	Transcr. at gene 5' and 3'	K562	blood
26	chr4:79700000-79705200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:79700000-79705200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:79700000-79708600	Weak transcription	A549	lung
29	chr4:79700200-79701600	Enhancers	Brain Cingulate Gyrus	brain
30	chr4:79700200-79701600	Enhancers	HSMMtube	muscle
31	chr4:79700200-79702000	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr4:79700200-79702000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr4:79700200-79702200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr4:79700200-79702200	Weak transcription	Brain Angular Gyrus	brain
35	chr4:79700200-79702200	Weak transcription	Left Ventricle	heart
36	chr4:79700200-79703000	Enhancers	Primary T cells from cord blood	blood
37	chr4:79700200-79703000	Enhancers	NHEK	skin
38	chr4:79700200-79714200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr4:79700200-79732800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr4:79700400-79701600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:79700400-79702200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:79700400-79702400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr4:79700400-79702400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr4:79700400-79702600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:79700400-79702600	Weak transcription	Small Intestine	intestine
46	chr4:79700400-79704600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:79700400-79704600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:79700400-79707800	Weak transcription	Brain Germinal Matrix	brain
49	chr4:79700400-79718200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr4:79700600-79701600	Enhancers	Duodenum Smooth Muscle	Duodenum

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