Variant report

Variant	rs6699241
Chromosome Location	chr1:171282759-171282760
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	CEBPB	chr1:171282717-171283709	HCT-116	colon:	n/a	chr1:171282864-171282877
2	CTCF	chr1:171282728-171283302	H1-hESC	embryonic stem cell:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
3	RAD21	chr1:171282734-171283412	H1-hESC	embryonic stem cell:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
4	RAD21	chr1:171282655-171283383	H1-hESC	embryonic stem cell:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
5	RAD21	chr1:171282542-171283561	SK-N-SH	brain:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
6	RAD21	chr1:171282562-171283551	HCT-116	colon:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
7	TBP	chr1:171282759-171283671	GM12878	blood:	n/a	n/a
8	RAD21	chr1:171282600-171283349	GM12878	blood:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
9	REST	chr1:171282700-171283321	PFSK-1	brain:	n/a	chr1:171282872-171282885 chr1:171283021-171283030 chr1:171282870-171282888
10	RAD21	chr1:171282743-171283374	Hela-S3	cervix:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
11	REST	chr1:171282703-171283619	HL-60	blood:	n/a	chr1:171282872-171282885 chr1:171283021-171283030 chr1:171282870-171282888
12	CTCF	chr1:171282758-171283365	IMR90	lung:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
13	CTCF	chr1:171282712-171283360	GM12878	blood:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
14	SMC3	chr1:171282652-171283385	GM12878	blood:	n/a	chr1:171282875-171282889
15	MAX	chr1:171282599-171283469	NB4	blood:	n/a	chr1:171283160-171283170
16	BHLHE40	chr1:171282485-171283453	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr1:171282597-171283462	GM12878	blood:	n/a	n/a
18	CTCF	chr1:171282720-171282870	HFF	foreskin:	n/a	n/a
19	RAD21	chr1:171282613-171283359	MCF-7	breast:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
20	CTCF	chr1:171282737-171283247	HepG2	liver:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
21	RAD21	chr1:171282757-171283310	SK-N-SH_RA	brain:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
22	ATF2	chr1:171282746-171283366	GM12878	blood:	n/a	n/a
23	SMC3	chr1:171282498-171283454	SK-N-SH	brain:	n/a	chr1:171282875-171282889
24	JUN	chr1:171282712-171283212	H1-hESC	embryonic stem cell:	n/a	chr1:171282913-171282922
25	CTCF	chr1:171282627-171283455	MCF-7	breast:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
26	EP300	chr1:171282569-171283417	GM12878	blood:	n/a	n/a
27	RAD21	chr1:171282703-171283453	H1-hESC	embryonic stem cell:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
28	RUNX3	chr1:171282487-171283311	GM12878	blood:	n/a	n/a
29	RAD21	chr1:171282602-171283588	MCF-7	breast:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
30	RELA	chr1:171282490-171283436	GM19099	blood:	n/a	n/a
31	SMC3	chr1:171282713-171283385	Hela-S3	cervix:	n/a	chr1:171282875-171282889
32	CTCF	chr1:171282602-171283445	MCF-7	breast:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
33	CTCF	chr1:171282385-171283538	A549	lung:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
34	RAD21	chr1:171282585-171283617	HCT-116	colon:	n/a	chr1:171282871-171282890 chr1:171283120-171283139
35	EBF1	chr1:171282593-171282863	GM12878	blood:	n/a	n/a
36	CTCF	chr1:171282426-171283466	HCT-116	colon:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
37	CTCF	chr1:171282544-171283407	HCT-116	colon:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
38	ZNF143	chr1:171282743-171283327	GM12878	blood:	n/a	n/a
39	STAT1	chr1:171282704-171283312	GM12878	blood:	n/a	chr1:171282914-171282922
40	REST	chr1:171282716-171283320	MCF-7	breast:	n/a	chr1:171282872-171282885 chr1:171283021-171283030 chr1:171282870-171282888
41	CTCF	chr1:171282657-171283283	T-47D	breast:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
42	CTCF	chr1:171282501-171283705	SK-N-SH	brain:	n/a	chr1:171283122-171283140 chr1:171283117-171283138 chr1:171282873-171282891 chr1:171282868-171282889
43	RUNX3	chr1:171282477-171282840	GM12878	blood:	n/a	n/a
44	MEF2C	chr1:171282575-171283335	GM12878	blood:	n/a	chr1:171282833-171282849 chr1:171282836-171282847 chr1:171282834-171282848 chr1:171282829-171282850 chr1:171282836-171282845 chr1:171282829-171282850 chr1:171282834-171282849 chr1:171282833-171282848 chr1:171282834-171282849 chr1:171283065-171283086 chr1:171282835-171282846 chr1:171283046-171283054
45	EP300	chr1:171282556-171283499	GM12878	blood:	n/a	n/a
46	MEF2A	chr1:171282651-171283432	GM12878	blood:	n/a	chr1:171282833-171282849 chr1:171282836-171282847 chr1:171282834-171282848 chr1:171282829-171282850 chr1:171282836-171282845 chr1:171282829-171282850 chr1:171282834-171282849 chr1:171282833-171282848 chr1:171282834-171282849 chr1:171283065-171283086 chr1:171282835-171282846 chr1:171283046-171283054
47	KAP1	chr1:171282660-171283514	HEK293	kidney:	n/a	n/a
48	MAX	chr1:171282754-171283471	MCF-7	breast:	n/a	chr1:171283160-171283170
49	STAT3	chr1:171282570-171283276	GM12878	blood:	n/a	chr1:171282914-171282922

No.	Distal block	Cell Line	Cell type
1	chr1:171282676..171283284-chr1:171373985..171374977,4	MCF-7	breast:
2	chr1:170935849..170936463-chr1:171282647..171283201,2	MCF-7	breast:
3	chr1:170936062..170936908-chr1:171282571..171283243,3	MCF-7	breast:

Variant related genes	Relation type
FMO4	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16864312	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16864314	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16864332	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16864353	1.00[ASN][1000 genomes]
rs16864359	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16864362	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16864364	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16864368	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16864389	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[ASN][1000 genomes]
rs16864392	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs16864395	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs16864396	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs16864417	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2038097	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28360425	1.00[ASN][1000 genomes]
rs28360434	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28360435	1.00[ASN][1000 genomes]
rs45443493	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs45552133	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs45579736	0.86[AFR][1000 genomes]
rs58887979	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6674736	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6685422	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs717023	1.00[JPT][hapmap];0.93[YRI][hapmap]
rs717024	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs7543159	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	52 gene(s)	inside rSNPs	diseases
3	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171266600-171288400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:171280000-171283400	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr1:171280400-171282800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:171280400-171283200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:171280400-171283200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:171280600-171282800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:171280800-171283600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:171282400-171282800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:171282400-171282800	Enhancers	Fetal Intestine Small	intestine
10	chr1:171282400-171283000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:171282400-171283200	Enhancers	H9 Cell Line	embryonic stem cell
12	chr1:171282400-171283400	Enhancers	Primary B cells from peripheral blood	blood
13	chr1:171282400-171284200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:171282600-171282800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:171282600-171282800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:171282600-171282800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:171282600-171282800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:171282600-171282800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:171282600-171282800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:171282600-171282800	Enhancers	Aorta	Aorta
21	chr1:171282600-171282800	Enhancers	Colon Smooth Muscle	Colon
22	chr1:171282600-171282800	Enhancers	Duodenum Mucosa	Duodenum
23	chr1:171282600-171282800	Enhancers	Fetal Intestine Large	intestine
24	chr1:171282600-171282800	Enhancers	Fetal Kidney	kidney
25	chr1:171282600-171282800	Enhancers	Stomach Smooth Muscle	stomach
26	chr1:171282600-171282800	Enhancers	Dnd41	blood
27	chr1:171282600-171282800	Enhancers	Hela-S3	cervix
28	chr1:171282600-171282800	Enhancers	NH-A	brain
29	chr1:171282600-171282800	Enhancers	NHLF	lung
30	chr1:171282600-171283000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:171282600-171283000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:171282600-171283000	Enhancers	Primary B cells from cord blood	blood
33	chr1:171282600-171283000	Enhancers	Liver	Liver
34	chr1:171282600-171283200	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr1:171282600-171283200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr1:171282600-171283200	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr1:171282600-171283200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:171282600-171283200	Enhancers	Fetal Heart	heart
39	chr1:171282600-171283400	Enhancers	Stomach Mucosa	stomach
40	chr1:171282600-171283600	Active TSS	NHDF-Ad	bronchial
41	chr1:171282600-171283800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:171282600-171284000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr1:171282600-171284200	Active TSS	Duodenum Smooth Muscle	Duodenum

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