Variant report

Variant	rs1771475
Chromosome Location	chr1:228298564-228298565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL3	chr1:228297558-228298588	GM12878	blood:	n/a	n/a
2	JUN	chr1:228296050-228298705	K562	blood:	n/a	n/a
3	POLR2A	chr1:228295848-228298694	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:228297992..228299811-chr1:228608670..228610850,2	K562	blood:
2	chr1:228297957..228299984-chr1:228304841..228307293,2	K562	blood:
3	chr1:228295318..228298683-chr1:228360322..228363984,4	K562	blood:
4	chr1:228266682..228273620-chr1:228293839..228298603,9	MCF-7	breast:
5	chr1:228293945..228298846-chr1:228325398..228330582,13	K562	blood:
6	chr1:228294705..228298588-chr1:228325821..228329680,6	MCF-7	breast:
7	chr1:228295286..228298610-chr1:228351640..228355026,4	K562	blood:
8	chr1:228288384..228298705-chr1:228351640..228357240,26	K562	blood:
9	chr1:228295585..228298584-chr1:228645620..228647778,2	K562	blood:
10	chr1:228293945..228298682-chr1:228326047..228331152,9	K562	blood:
11	chr1:228282584..228285424-chr1:228297065..228299503,2	MCF-7	breast:

No data

Variant related genes	Relation type
MRPL55	TF binding region
ENSG00000143761	Chromatin interaction
ENSG00000264944	Chromatin interaction
ENSG00000143774	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000203684	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10916269	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1094601	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1188976	0.85[ASW][hapmap];0.94[LWK][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1771454	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs1771466	0.92[ASW][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap]
rs1856871	0.87[AFR][1000 genomes]
rs1934882	0.81[YRI][hapmap]
rs4653534	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6686210	0.86[YRI][hapmap]
rs6698730	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs73092925	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7534419	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs822728	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822729	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822730	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822731	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822732	0.92[ASW][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap]
rs822735	0.83[AMR][1000 genomes]
rs822737	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs822741	0.92[ASW][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap]
rs822742	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs849750	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs947086	0.92[ASW][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228296600-228298600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:228297600-228298800	Flanking Active TSS	K562	blood
3	chr1:228297800-228298800	Enhancers	Stomach Mucosa	stomach
4	chr1:228298000-228298600	Flanking Active TSS	Duodenum Mucosa	Duodenum
5	chr1:228298000-228298600	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr1:228298000-228298600	Flanking Active TSS	HSMM	muscle
7	chr1:228298000-228298600	Enhancers	HUVEC	blood vessel
8	chr1:228298000-228301000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:228298000-228301400	Weak transcription	Primary T cells from cord blood	blood
10	chr1:228298200-228298600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:228298200-228298600	Enhancers	Fetal Kidney	kidney
12	chr1:228298200-228298600	Enhancers	Pancreas	Pancrea
13	chr1:228298200-228298600	Flanking Active TSS	HepG2	liver
14	chr1:228298200-228298800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:228298200-228298800	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr1:228298200-228299000	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr1:228298200-228299600	Enhancers	Fetal Intestine Large	intestine
18	chr1:228298200-228299800	Enhancers	Placenta	Placenta
19	chr1:228298200-228301200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:228298200-228301400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:228298200-228302600	Weak transcription	Fetal Heart	heart
22	chr1:228298200-228303800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:228298200-228304600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:228298200-228307200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:228298400-228298600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:228298400-228298600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:228298400-228298600	Enhancers	Colon Smooth Muscle	Colon
28	chr1:228298400-228298600	Bivalent/Poised TSS	Thymus	Thymus
29	chr1:228298400-228298800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:228298400-228298800	Enhancers	HSMMtube	muscle
31	chr1:228298400-228300000	Enhancers	Fetal Intestine Small	intestine
32	chr1:228298400-228307200	Weak transcription	NHEK	skin

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