Variant report

Variant	rs41270181
Chromosome Location	chr1:228332481-228332482
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	TAL1	chr1:228332332-228332720	K562	blood:	n/a	n/a
2	MYC	chr1:228332438-228332583	MCF-7	breast:	n/a	chr1:228332514-228332525 chr1:228332515-228332524
3	POLR2A	chr1:228332372-228333985	K562	blood:	n/a	n/a
4	MAX	chr1:228332090-228332752	K562	blood:	n/a	chr1:228332514-228332525 chr1:228332515-228332524
5	POLR2A	chr1:228332025-228332528	K562	blood:	n/a	n/a
6	POLR2A	chr1:228331544-228333910	K562	blood:	n/a	n/a
7	MYC	chr1:228332351-228332648	K562	blood:	n/a	chr1:228332514-228332525 chr1:228332515-228332524
8	MYC	chr1:228332307-228332741	K562	blood:	n/a	chr1:228332514-228332525 chr1:228332515-228332524
9	MAX	chr1:228332388-228332655	K562	blood:	n/a	chr1:228332514-228332525 chr1:228332515-228332524
10	POLR2A	chr1:228332009-228332563	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228331165..228333412-chr1:228361433..228363518,2	MCF-7	breast:
2	chr1:228284520..228292111-chr1:228324853..228335412,14	K562	blood:

Variant related genes	Relation type
GUK1	TF binding region
ENSG00000264944	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000143793	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs16848361	1.00[EUR][1000 genomes]
rs2231711	1.00[EUR][1000 genomes]
rs34658204	1.00[EUR][1000 genomes]
rs41314262	1.00[EUR][1000 genomes]
rs45460992	1.00[EUR][1000 genomes]
rs56280452	1.00[EUR][1000 genomes]
rs56394518	1.00[EUR][1000 genomes]
rs57624754	1.00[EUR][1000 genomes]
rs58696607	1.00[EUR][1000 genomes]
rs58787263	1.00[EUR][1000 genomes]
rs60538700	1.00[EUR][1000 genomes]
rs60642596	1.00[EUR][1000 genomes]
rs60777646	1.00[EUR][1000 genomes]
rs61091413	1.00[EUR][1000 genomes]
rs73108778	1.00[EUR][1000 genomes]
rs74140818	1.00[EUR][1000 genomes]
rs74140819	1.00[EUR][1000 genomes]
rs74140821	1.00[EUR][1000 genomes]
rs74140822	1.00[EUR][1000 genomes]
rs74140823	1.00[EUR][1000 genomes]
rs74140994	1.00[EUR][1000 genomes]
rs74143607	1.00[EUR][1000 genomes]
rs74143612	1.00[EUR][1000 genomes]
rs74143614	1.00[EUR][1000 genomes]
rs74143615	1.00[EUR][1000 genomes]
rs74143616	1.00[EUR][1000 genomes]
rs8192631	1.00[EUR][1000 genomes]
rs9662484	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
5	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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
6	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
8	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
9	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
10	nsv873256	chr1:228322826-228359775	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
11	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
12	nsv549288	chr1:228327659-228363750	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
13	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228329000-228336800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:228329000-228339400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:228329000-228339600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:228329200-228332600	Enhancers	Placenta Amnion	Placenta Amnion
5	chr1:228329200-228337400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:228329400-228333200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:228329400-228333800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:228329400-228333800	Genic enhancers	Spleen	Spleen
9	chr1:228329400-228336600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:228329400-228337600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:228329400-228337600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:228329400-228338200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:228329600-228332800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:228329600-228335200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:228329600-228335600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:228329600-228336800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:228329800-228332600	Enhancers	Brain Anterior Caudate	brain
18	chr1:228329800-228332800	Enhancers	Liver	Liver
19	chr1:228329800-228336400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:228329800-228336600	Weak transcription	A549	lung
21	chr1:228330000-228332600	Enhancers	Primary T cells from cord blood	blood
22	chr1:228330000-228332600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:228330000-228332600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:228330000-228332600	Enhancers	Left Ventricle	heart
25	chr1:228330000-228332600	Enhancers	Stomach Mucosa	stomach
26	chr1:228330000-228332800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:228330000-228333200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:228330000-228333600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr1:228330000-228334800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:228330000-228335800	Weak transcription	Fetal Lung	lung
31	chr1:228330000-228337200	Genic enhancers	Fetal Muscle Leg	muscle
32	chr1:228330000-228337800	Genic enhancers	Lung	lung
33	chr1:228330200-228333200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:228330200-228333200	Genic enhancers	Gastric	stomach
35	chr1:228330200-228333200	Enhancers	Right Ventricle	heart
36	chr1:228330200-228333400	Genic enhancers	Stomach Smooth Muscle	stomach
37	chr1:228330200-228333600	Weak transcription	Ovary	ovary
38	chr1:228330200-228336200	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:228330400-228332600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr1:228330400-228333000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr1:228330400-228333200	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr1:228330400-228333200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:228330400-228333400	Weak transcription	Aorta	Aorta
44	chr1:228330600-228332800	Enhancers	Adipose Nuclei	Adipose
45	chr1:228330600-228333400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:228330600-228337200	Genic enhancers	Fetal Muscle Trunk	muscle
47	chr1:228330800-228332600	Enhancers	Primary B cells from peripheral blood	blood
48	chr1:228330800-228332600	Genic enhancers	Fetal Intestine Small	intestine
49	chr1:228330800-228332600	Enhancers	Placenta	Placenta
50	chr1:228330800-228332600	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links