Variant report

Variant	rs822728
Chromosome Location	chr1:228275661-228275662
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	POLR2A	chr1:228274391-228275988	A549	lung:	n/a	n/a
2	POLR2A	chr1:228274276-228290284	K562	blood:	n/a	n/a
3	POLR2A	chr1:228274933-228281306	GM12878	blood:	n/a	n/a
4	MAX	chr1:228275559-228275991	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr1:228275627-228277219	HL-60	blood:	n/a	n/a
6	CTCF	chr1:228275600-228275750	BJ	skin:	n/a	n/a
7	STAT3	chr1:228275627-228275871	MCF10A-Er-Src	breast:	n/a	n/a
8	MAX	chr1:228275618-228275809	Hela-S3	cervix:	n/a	n/a
9	HEY1	chr1:228275494-228276138	K562	blood:	n/a	n/a
10	MAX	chr1:228275548-228276092	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr1:228275218-228276108	SK-N-MC	brain:	n/a	n/a
12	TBL1XR1	chr1:228275574-228275898	GM12878	blood:	n/a	n/a
13	EBF1	chr1:228275633-228276215	GM12878	blood:	n/a	n/a
14	MYC	chr1:228275472-228275904	MCF10A-Er-Src	breast:	n/a	n/a
15	CTCF	chr1:228275640-228275790	HVMF	connective:	n/a	n/a
16	MAX	chr1:228275481-228276003	NB4	blood:	n/a	n/a
17	POLR2A	chr1:228275546-228276101	GM12891	blood:	n/a	n/a
18	JUND	chr1:228275661-228275763	K562	blood:	n/a	chr1:228275707-228275715 chr1:228275709-228275718
19	ZNF263	chr1:228275596-228275946	HEK293-T-REx	kidney:	n/a	chr1:228275753-228275762
20	JUND	chr1:228275070-228276122	SK-N-SH	brain:	n/a	chr1:228275707-228275715 chr1:228275709-228275718
21	POLR2A	chr1:228275592-228275922	HUVEC	blood vessel:	n/a	n/a
22	FOS	chr1:228275468-228275900	MCF10A-Er-Src	breast:	n/a	chr1:228275707-228275715 chr1:228275708-228275719 chr1:228275709-228275718
23	POLR2A	chr1:228274778-228276243	PFSK-1	brain:	n/a	n/a
24	CTCF	chr1:228275540-228275690	AG09309	skin:	n/a	n/a
25	E2F4	chr1:228275411-228275698	MCF10A-Er-Src	breast:	n/a	n/a
26	CTCF	chr1:228275520-228275670	HPAF	blood vessel:	n/a	n/a
27	POLR2A	chr1:228275165-228276140	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr1:228275358-228275924	SK-N-SH	brain:	n/a	n/a
29	CTCF	chr1:228275520-228275670	HCM	heart:	n/a	n/a
30	POLR2A	chr1:228275404-228276049	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr1:228275637-228275822	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr1:228275359-228276139	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr1:228275260-228276174	GM12892	blood:	n/a	n/a
34	STAT3	chr1:228275537-228275853	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr1:228274170-228289426	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:228275325-228276210	Hela-S3	cervix:	n/a	n/a
37	MAZ	chr1:228275086-228275944	IMR90	lung:	n/a	n/a
38	POLR2A	chr1:228275073-228276201	GM12878	blood:	n/a	n/a
39	MAX	chr1:228275462-228276088	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr1:228275485-228275774	MCF10A-Er-Src	breast:	n/a	n/a
41	MXI1	chr1:228275384-228275887	GM12878	blood:	n/a	n/a
42	FOS	chr1:228275368-228275890	MCF10A-Er-Src	breast:	n/a	chr1:228275707-228275715 chr1:228275708-228275719 chr1:228275709-228275718
43	MYC	chr1:228275449-228275904	MCF10A-Er-Src	breast:	n/a	n/a
44	FOS	chr1:228275478-228275893	MCF10A-Er-Src	breast:	n/a	chr1:228275707-228275715 chr1:228275708-228275719 chr1:228275709-228275718
45	CTCF	chr1:228275520-228275670	AoAF	blood vessel:	n/a	n/a
46	FOSL2	chr1:228275360-228276031	SK-N-SH	brain:	n/a	chr1:228275707-228275715 chr1:228275709-228275718
47	CTCF	chr1:228275520-228275670	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr1:228275590-228276198	K562	blood:	n/a	n/a
49	POLR2A	chr1:228275569-228276085	GM12891	blood:	n/a	n/a
50	GABPA	chr1:228275493-228276156	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228274188..228275817-chr1:228326057..228328132,2	MCF-7	breast:
2	chr1:228274118..228278669-chr1:228294195..228297645,6	MCF-7	breast:
3	chr1:228275377..228276887-chr1:228353250..228355389,2	K562	blood:

Variant related genes	Relation type
ARF1	TF binding region
ENSG00000143774	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000181873	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10916269	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1094601	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1188976	0.85[ASW][hapmap];0.94[LWK][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1771454	0.82[YRI][hapmap]
rs1771466	0.92[ASW][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs1771475	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]
rs1856871	0.84[AFR][1000 genomes]
rs4653534	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6686210	0.82[YRI][hapmap]
rs6698730	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs73092925	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7534419	0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs822729	0.95[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];0.86[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822732	0.92[ASW][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs822735	0.83[AMR][1000 genomes]
rs822737	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs822741	0.92[ASW][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs822742	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs849750	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs947086	0.92[ASW][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228271600-228278600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr1:228272000-228275800	Enhancers	Spleen	Spleen
3	chr1:228272400-228279400	Genic enhancers	Fetal Muscle Leg	muscle
4	chr1:228272400-228280000	Genic enhancers	Fetal Thymus	thymus
5	chr1:228272400-228284400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:228272600-228278400	Enhancers	Small Intestine	intestine
7	chr1:228272600-228280200	Enhancers	Fetal Heart	heart
8	chr1:228272800-228278600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:228272800-228278600	Genic enhancers	Fetal Stomach	stomach
10	chr1:228273000-228275800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:228273000-228276000	Enhancers	Placenta	Placenta
12	chr1:228273000-228277400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:228273000-228279200	Genic enhancers	Fetal Intestine Small	intestine
14	chr1:228273000-228284200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:228273200-228275800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:228273200-228275800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:228273200-228275800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:228273200-228276400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:228273200-228276400	Enhancers	Stomach Mucosa	stomach
20	chr1:228273400-228275800	Enhancers	Lung	lung
21	chr1:228273400-228275800	Enhancers	Right Ventricle	heart
22	chr1:228273400-228275800	Enhancers	HSMMtube	muscle
23	chr1:228273400-228276200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:228273400-228276400	Enhancers	Brain Angular Gyrus	brain
25	chr1:228273400-228276600	Weak transcription	Brain Germinal Matrix	brain
26	chr1:228273400-228277600	Enhancers	Brain Cingulate Gyrus	brain
27	chr1:228273400-228278200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:228273400-228279000	Genic enhancers	HepG2	liver
29	chr1:228273400-228280200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr1:228273400-228285200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:228273600-228275800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:228273600-228275800	Enhancers	Rectal Smooth Muscle	rectum
33	chr1:228273600-228276000	Enhancers	Aorta	Aorta
34	chr1:228273600-228276400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:228273600-228277200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr1:228273600-228277400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:228273600-228277800	Genic enhancers	Dnd41	blood
38	chr1:228273600-228278200	Weak transcription	Fetal Brain Male	brain
39	chr1:228273600-228278200	Genic enhancers	K562	blood
40	chr1:228273600-228281800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:228273800-228275800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:228273800-228275800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:228273800-228275800	Enhancers	Brain Anterior Caudate	brain
44	chr1:228273800-228276200	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr1:228273800-228279200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:228274000-228275800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:228274000-228279200	Enhancers	Colon Smooth Muscle	Colon
48	chr1:228274000-228280600	Enhancers	Psoas Muscle	Psoas
49	chr1:228274200-228281200	Genic enhancers	Liver	Liver
50	chr1:228274400-228275800	Enhancers	Fetal Kidney	kidney

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