Variant report

Variant	rs1870012
Chromosome Location	chr5:59996206-59996207
allele	C/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	NFYB	chr5:59995554-59996449	Hela-S3	cervix:	n/a	chr5:59996013-59996028 chr5:59996014-59996028 chr5:59996015-59996030 chr5:59996013-59996028
2	ZBTB7A	chr5:59995828-59996240	K562	blood:	n/a	n/a
3	KAP1	chr5:59995333-59996536	HEK293	kidney:	n/a	n/a
4	STAT1	chr5:59995406-59996279	GM12878	blood:	n/a	n/a
5	SRF	chr5:59995789-59996238	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr5:59995404-59996524	ECC-1	luminal epithelium:	n/a	n/a
7	HEY1	chr5:59995185-59996646	K562	blood:	n/a	chr5:59995936-59995951 chr5:59995842-59995857 chr5:59996024-59996039
8	NFYA	chr5:59995596-59996236	K562	blood:	n/a	chr5:59996013-59996028 chr5:59996014-59996028 chr5:59996013-59996028
9	JUND	chr5:59996051-59996245	H1-hESC	embryonic stem cell:	n/a	n/a
10	YY1	chr5:59995343-59996383	HepG2	liver:	n/a	chr5:59996023-59996032 chr5:59995933-59995947
11	EP300	chr5:59995809-59996283	GM12878	blood:	n/a	chr5:59996002-59996018
12	MAX	chr5:59995225-59996649	K562	blood:	n/a	n/a
13	CREB1	chr5:59995293-59996595	HepG2	liver:	n/a	n/a
14	POLR2A	chr5:59995292-59996599	H1-neurons	neurons:	n/a	n/a
15	POLR2A	chr5:59995284-59996921	K562	blood:	n/a	n/a
16	POLR2A	chr5:59995273-59996555	Hela-S3	cervix:	n/a	n/a
17	ATF1	chr5:59995447-59996702	K562	blood:	n/a	n/a
18	TAF1	chr5:59995702-59996331	GM12878	blood:	n/a	n/a
19	POLR2A	chr5:59995328-59996556	Raji	blood:	n/a	n/a
20	MYC	chr5:59995284-59996677	K562	blood:	n/a	n/a
21	TCF7L2	chr5:59995243-59996475	Hela-S3	cervix:	n/a	n/a
22	CTBP2	chr5:59995369-59996427	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr5:59995227-59997036	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr5:59995341-59996298	GM12878	blood:	n/a	n/a
25	ZC3H11A	chr5:59995805-59996522	K562	blood:	n/a	n/a
26	MXI1	chr5:59995362-59996570	K562	blood:	n/a	n/a
27	PML	chr5:59995301-59996595	MCF-7	breast:	n/a	n/a
28	HCFC1	chr5:59994863-59996773	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr5:59995435-59996321	HUVEC	blood vessel:	n/a	n/a
30	HEY1	chr5:59995356-59996468	K562	blood:	n/a	chr5:59995936-59995951 chr5:59995842-59995857 chr5:59996024-59996039
31	MAX	chr5:59995202-59996774	HCT-116	colon:	n/a	n/a
32	TBP	chr5:59995466-59996218	Hela-S3	cervix:	n/a	n/a
33	MAX	chr5:59995220-59996639	NB4	blood:	n/a	n/a
34	POLR2A	chr5:59995426-59996478	GM12878	blood:	n/a	n/a
35	GABPA	chr5:59995798-59996276	HL-60	blood:	n/a	n/a
36	ETS1	chr5:59995418-59996225	K562	blood:	n/a	chr5:59996042-59996051 chr5:59996038-59996054 chr5:59996042-59996051 chr5:59996042-59996051 chr5:59996042-59996051 chr5:59996042-59996051
37	TAF1	chr5:59995359-59996490	K562	blood:	n/a	n/a
38	MTA3	chr5:59994872-59996687	GM12878	blood:	n/a	n/a
39	PML	chr5:59995412-59996645	K562	blood:	n/a	n/a
40	REST	chr5:59995618-59996259	HL-60	blood:	n/a	chr5:59996092-59996105
41	SIN3AK20	chr5:59995206-59996212	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr5:59995639-59996263	GM12891	blood:	n/a	n/a
43	POLR2A	chr5:59995742-59996252	HepG2	liver:	n/a	n/a
44	MYC	chr5:59995392-59996346	MCF-7	breast:	n/a	n/a
45	POLR2A	chr5:59995480-59996383	HL-60	blood:	n/a	n/a
46	MAX	chr5:59995248-59996540	HCT-116	colon:	n/a	n/a
47	FOXP2	chr5:59995729-59996259	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr5:59995318-59996812	HepG2	liver:	n/a	n/a
49	ELF1	chr5:59995654-59996259	K562	blood:	n/a	chr5:59996038-59996051 chr5:59995933-59995945
50	CREB1	chr5:59995331-59996379	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:75385509..75386409-chr5:59996058..59996562,2	HCT-116	colon:
2	chr5:59994474..59997876-chr5:60455928..60460228,5	K562	blood:
3	chr5:59995106..59997535-chr5:60240120..60242292,3	K562	blood:
4	chr5:59994210..59996553-chr5:60627404..60629725,2	MCF-7	breast:
5	chr5:59995886..59998322-chr5:60239584..60242446,2	MCF-7	breast:

Variant related genes	Relation type
DEPDC1B	TF binding region
ENSG00000251279	Chromatin interaction
ENSG00000049167	Chromatin interaction
ENSG00000130449	Chromatin interaction
ENSG00000188725	Chromatin interaction
ENSG00000268584	Chromatin interaction
ENSG00000164182	Chromatin interaction
ENSG00000166348	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1026418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1107232	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1107233	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs12658660	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1379111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1379113	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1460959	1.00[CHB][hapmap]
rs1563516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1563517	1.00[CHB][hapmap]
rs1563518	1.00[CHB][hapmap]
rs1563519	1.00[CHB][hapmap]
rs1563905	1.00[CHB][hapmap]
rs1563906	1.00[CHB][hapmap]
rs1563907	1.00[CHB][hapmap]
rs16878304	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs16878315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16878354	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1870013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1992613	1.00[CHB][hapmap]
rs2045355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2061254	1.00[CEU][hapmap]
rs2124751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2124753	0.81[ASN][1000 genomes]
rs2169254	1.00[CHB][hapmap]
rs2305680	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2591635	1.00[CEU][hapmap]
rs2606688	1.00[CEU][hapmap]
rs286150	1.00[CEU][hapmap]
rs286152	1.00[CEU][hapmap]
rs286157	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2898298	1.00[CHB][hapmap]
rs34414908	0.81[ASN][1000 genomes]
rs34915115	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3857238	1.00[CHB][hapmap]
rs4273559	1.00[CHB][hapmap]
rs61752571	0.83[ASN][1000 genomes]
rs6871928	1.00[CHB][hapmap]
rs6872509	1.00[CEU][hapmap]
rs7702459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7706896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7708849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7712043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7713586	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7713673	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7716051	1.00[CHB][hapmap]
rs7719525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7733069	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs897671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs897673	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462198	chr5:59969015-60116613	Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv598298	chr5:59969015-60116613	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1023403	chr5:59969534-60079822	Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv4850	chr5:59976186-60039810	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv508362	chr5:59990308-60050894	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	esv1816307	chr5:59992305-60012235	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	esv1794154	chr5:59995393-60012235	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	esv1821070	chr5:59995393-60012235	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	esv1801919	chr5:59995393-60013913	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59992600-59996600	Active TSS	GM12878-XiMat	blood
2	chr5:59993000-59996400	Active TSS	Placenta	Placenta
3	chr5:59994200-59996400	Active TSS	Fetal Kidney	kidney
4	chr5:59994200-59996600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:59994200-59996800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:59994400-59996600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:59994400-59996600	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr5:59994400-59996600	Active TSS	K562	blood
9	chr5:59994400-59996800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr5:59994400-59996800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:59994400-59997000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr5:59994600-59996600	Active TSS	H1 Cell Line	embryonic stem cell
13	chr5:59994600-59996800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:59994600-59996800	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr5:59994600-59996800	Active TSS	NHLF	lung
16	chr5:59994800-59996600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr5:59994800-59996600	Active TSS	H9 Cell Line	embryonic stem cell
18	chr5:59994800-59996600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:59994800-59996600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:59994800-59996600	Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr5:59994800-59996600	Active TSS	Fetal Intestine Small	intestine
22	chr5:59994800-59996800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:59994800-59996800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:59994800-59996800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:59994800-59996800	Active TSS	HSMM	muscle
26	chr5:59994800-59996800	Active TSS	HSMMtube	muscle
27	chr5:59994800-59996800	Active TSS	NHDF-Ad	bronchial
28	chr5:59994800-59997000	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr5:59994800-59997000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:59994800-59997000	Active TSS	Fetal Brain Female	brain
31	chr5:59994800-59997000	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr5:59995000-59996400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:59995000-59996400	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr5:59995000-59996400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:59995000-59996400	Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr5:59995000-59996400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:59995000-59996400	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr5:59995000-59996400	Bivalent/Poised TSS	HepG2	liver
39	chr5:59995000-59996600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:59995000-59996600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:59995000-59996600	Active TSS	Muscle Satellite Cultured Cells	--
42	chr5:59995000-59996600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:59995000-59996600	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr5:59995000-59996600	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr5:59995000-59996600	Active TSS	Fetal Intestine Large	intestine
46	chr5:59995000-59996600	Active TSS	Stomach Mucosa	stomach
47	chr5:59995000-59996600	Active TSS	Spleen	Spleen
48	chr5:59995000-59996600	Active TSS	NH-A	brain
49	chr5:59995000-59996800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:59995000-59996800	Active TSS	Colonic Mucosa	Colon

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