Variant report

Variant	rs17131260
Chromosome Location	chr1:70820313-70820314
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:457)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:457 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:70820240-70820819	GM12878	blood:	n/a	n/a
2	TAF1	chr1:70819662-70820901	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr1:70820085-70821098	K562	blood:	n/a	n/a
4	MAX	chr1:70820057-70820852	K562	blood:	n/a	chr1:70820464-70820474
5	ATF2	chr1:70820141-70820996	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:70820015-70820836	MCF-7	breast:	n/a	n/a
7	SIN3A	chr1:70819043-70820956	H1-hESC	embryonic stem cell:	n/a	chr1:70820145-70820154
8	EP300	chr1:70820237-70821093	K562	blood:	n/a	n/a
9	GABPA	chr1:70820080-70821044	HL-60	blood:	n/a	n/a
10	ELF1	chr1:70819973-70820891	GM12878	blood:	n/a	chr1:70820092-70820101 chr1:70820392-70820403
11	RELA	chr1:70820046-70821128	GM10847	blood:	n/a	n/a
12	YY1	chr1:70819991-70820841	A549	lung:	n/a	chr1:70820092-70820101 chr1:70820382-70820402 chr1:70820386-70820394
13	GATA3	chr1:70820003-70820941	SK-N-SH	brain:	n/a	n/a
14	MXI1	chr1:70820203-70820824	K562	blood:	n/a	n/a
15	TBP	chr1:70819690-70821073	K562	blood:	n/a	n/a
16	GTF2F1	chr1:70820200-70820827	K562	blood:	n/a	n/a
17	MAFK	chr1:70820154-70821052	HepG2	liver:	n/a	n/a
18	SIN3A	chr1:70820113-70820724	GM12878	blood:	n/a	chr1:70820145-70820154
19	MAX	chr1:70819593-70820980	SK-N-SH	brain:	n/a	chr1:70820464-70820474
20	BRCA1	chr1:70820007-70820985	H1-hESC	embryonic stem cell:	n/a	chr1:70820407-70820416
21	BCLAF1	chr1:70820266-70820936	K562	blood:	n/a	n/a
22	ELF1	chr1:70820308-70820706	K562	blood:	n/a	chr1:70820392-70820403
23	REST	chr1:70820173-70820749	SK-N-SH	brain:	n/a	n/a
24	RCOR1	chr1:70819921-70821135	K562	blood:	n/a	n/a
25	TAF1	chr1:70820168-70820652	GM12892	blood:	n/a	n/a
26	POLR2A	chr1:70819335-70821040	Hela-S3	cervix:	n/a	n/a
27	GATA3	chr1:70819462-70820647	MCF-7	breast:	n/a	n/a
28	MTA3	chr1:70819448-70821088	GM12878	blood:	n/a	n/a
29	FOXA1	chr1:70820275-70820559	T-47D	breast:	n/a	n/a
30	ELF1	chr1:70819424-70820829	GM12878	blood:	n/a	chr1:70820092-70820101 chr1:70820392-70820403
31	POLR2A	chr1:70820100-70820789	HepG2	liver:	n/a	n/a
32	TAF1	chr1:70819993-70820650	GM12892	blood:	n/a	n/a
33	YY1	chr1:70819992-70820798	NT2-D1	testis:	n/a	chr1:70820092-70820101 chr1:70820382-70820402 chr1:70820386-70820394
34	TAF1	chr1:70819959-70820732	Hela-S3	cervix:	n/a	n/a
35	JUND	chr1:70819849-70821087	K562	blood:	n/a	n/a
36	ETS1	chr1:70820219-70820682	K562	blood:	n/a	chr1:70820407-70820416
37	GABPA	chr1:70820196-70821066	SK-N-SH	brain:	n/a	n/a
38	YY1	chr1:70819957-70820686	H1-hESC	embryonic stem cell:	n/a	chr1:70820092-70820101 chr1:70820382-70820402 chr1:70820386-70820394
39	POLR2A	chr1:70819409-70820958	GM19193	blood:	n/a	n/a
40	JUND	chr1:70820243-70820767	HepG2	liver:	n/a	n/a
41	POLR2A	chr1:70819817-70821101	HepG2	liver:	n/a	n/a
42	UBTF	chr1:70819538-70820874	K562	blood:	n/a	n/a
43	STAT1	chr1:70820210-70820828	GM12878	blood:	n/a	chr1:70820489-70820497
44	POLR2A	chr1:70819921-70820863	HL-60	blood:	n/a	n/a
45	TEAD4	chr1:70820081-70821012	K562	blood:	n/a	n/a
46	EP300	chr1:70819912-70820968	ECC-1	luminal epithelium:	n/a	n/a
47	NFATC1	chr1:70820181-70820884	GM12878	blood:	n/a	n/a
48	HCFC1	chr1:70819192-70820893	K562	blood:	n/a	n/a
49	ZKSCAN1	chr1:70820047-70820954	Hela-S3	cervix:	n/a	n/a
50	ATF2	chr1:70820147-70821014	GM12878	blood:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70820102..70820781-chr15:65903328..65904070,2	Hela-S3	cervix:
2	chr1:70820291..70820901-chr2:219433432..219434034,2	Hela-S3	cervix:
3	chr1:70820185..70820796-chr5:57755458..57756161,2	Hela-S3	cervix:
4	chr1:70819842..70820538-chr21:44865952..44866901,2	Hela-S3	cervix:
5	chr1:70686799..70688622-chr1:70819236..70822047,3	K562	blood:
6	chr1:70820240..70820765-chr21:36228154..36229153,2	Hela-S3	cervix:
7	chr1:70670191..70673421-chr1:70819814..70822311,3	K562	blood:
8	chr1:70817791..70820390-chr1:70876768..70878594,3	MCF-7	breast:
9	chr1:70819015..70821620-chr1:70875663..70878848,3	MCF-7	breast:
10	chr1:70820223..70820900-chr8:22925930..22926635,2	Hela-S3	cervix:
11	chr1:70820287..70820857-chr20:33543072..33543925,2	Hela-S3	cervix:
12	chr1:70820288..70821043-chr14:55878152..55878652,2	Hela-S3	cervix:
13	chr1:70819013..70822302-chr1:70824014..70829303,9	MCF-7	breast:
14	chr1:70820288..70821087-chr12:13044176..13045013,2	Hela-S3	cervix:
15	chr1:70686799..70689606-chr1:70818481..70820974,3	K562	blood:
16	chr1:70685799..70687948-chr1:70819964..70821804,2	MCF-7	breast:
17	chr1:70819841..70820741-chr21:33765342..33765918,2	Hela-S3	cervix:
18	chr1:70686924..70688596-chr1:70820161..70821739,2	MCF-7	breast:
19	chr1:70814842..70821925-chr1:70874223..70879265,8	K562	blood:
20	chr1:70819966..70820788-chr12:46765760..46766512,2	Hela-S3	cervix:
21	chr1:70819774..70820742-chr19:2268884..2269581,2	Hela-S3	cervix:
22	chr1:70818087..70822177-chr1:70874224..70879265,8	K562	blood:
23	chr1:70819918..70820461-chr14:35515383..35516234,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
HHLA3	TF binding region
ENSG00000226088	Chromatin interaction
ENSG00000013588	Chromatin interaction
ENSG00000116754	Chromatin interaction
ENSG00000138614	Chromatin interaction
ENSG00000145632	Chromatin interaction
ENSG00000228988	Chromatin interaction
ENSG00000066557	Chromatin interaction
ENSG00000074621	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000188660	Chromatin interaction
ENSG00000116761	Chromatin interaction
ENSG00000256073	Chromatin interaction
ENSG00000159216	Chromatin interaction
ENSG00000120889	Chromatin interaction
ENSG00000151327	Chromatin interaction
ENSG00000126775	Chromatin interaction
ENSG00000144580	Chromatin interaction
ENSG00000100983	Chromatin interaction
ENSG00000167476	Chromatin interaction
ENSG00000104904	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11801679	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs11803222	1.00[EUR][1000 genomes]
rs17131275	1.00[EUR][1000 genomes]
rs17131277	1.00[EUR][1000 genomes]
rs17131278	1.00[EUR][1000 genomes]
rs17131280	1.00[EUR][1000 genomes]
rs17131282	1.00[EUR][1000 genomes]
rs17131286	1.00[EUR][1000 genomes]
rs17131287	1.00[EUR][1000 genomes]
rs17131288	1.00[EUR][1000 genomes]
rs17131289	1.00[EUR][1000 genomes]
rs17131292	1.00[EUR][1000 genomes]
rs58409087	0.81[AFR][1000 genomes]
rs59856193	1.00[EUR][1000 genomes]
rs61498338	0.87[AFR][1000 genomes]
rs6413468	1.00[EUR][1000 genomes]
rs72914697	1.00[EUR][1000 genomes]
rs72914698	1.00[EUR][1000 genomes]
rs72916616	1.00[EUR][1000 genomes]
rs72916621	1.00[EUR][1000 genomes]
rs72931208	1.00[EUR][1000 genomes]
rs7549628	1.00[EUR][1000 genomes]

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	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv1012563	chr1:70753332-70832118	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1801665	chr1:70755511-70832053	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 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	chr1:70817000-70821000	Active TSS	Fetal Brain Female	brain
2	chr1:70817600-70820600	Active TSS	Brain Angular Gyrus	brain
3	chr1:70817600-70821200	Active TSS	NHLF	lung
4	chr1:70817600-70821400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:70817600-70821600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:70817600-70822000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:70817800-70820800	Active TSS	GM12878-XiMat	blood
8	chr1:70817800-70821400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:70818000-70820600	Active TSS	NH-A	brain
10	chr1:70818000-70820800	Active TSS	Muscle Satellite Cultured Cells	--
11	chr1:70818000-70820800	Active TSS	Fetal Kidney	kidney
12	chr1:70818000-70820800	Active TSS	K562	blood
13	chr1:70818000-70820800	Active TSS	NHDF-Ad	bronchial
14	chr1:70818000-70821200	Active TSS	Brain Hippocampus Middle	brain
15	chr1:70818000-70821400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:70818000-70821400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr1:70818000-70821400	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr1:70818000-70821800	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr1:70818200-70821000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:70818200-70821000	Active TSS	Ovary	ovary
21	chr1:70818200-70821000	Active TSS	HSMM	muscle
22	chr1:70818200-70821200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:70818200-70821200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:70818200-70821200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:70818200-70821200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:70818200-70821200	Active TSS	Aorta	Aorta
27	chr1:70818200-70821200	Active TSS	Psoas Muscle	Psoas
28	chr1:70818200-70821200	Active TSS	Right Atrium	heart
29	chr1:70818200-70821200	Active TSS	Stomach Smooth Muscle	stomach
30	chr1:70818200-70821400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:70818200-70821400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:70818200-70821400	Active TSS	A549	lung
33	chr1:70818400-70820600	Active TSS	Fetal Thymus	thymus
34	chr1:70818400-70820800	Active TSS	NHEK	skin
35	chr1:70818400-70821000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:70818400-70821000	Active TSS	Fetal Intestine Large	intestine
37	chr1:70818400-70821200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr1:70818400-70821200	Active TSS	H1 Cell Line	embryonic stem cell
39	chr1:70818400-70821400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:70818600-70820800	Active TSS	Fetal Heart	heart
41	chr1:70818600-70820800	Active TSS	Thymus	Thymus
42	chr1:70818600-70820800	Active TSS	HSMMtube	muscle
43	chr1:70818600-70821000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:70818600-70821200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:70818600-70821200	Active TSS	Fetal Stomach	stomach
46	chr1:70818800-70820600	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr1:70818800-70820600	Active TSS	Fetal Muscle Leg	muscle
48	chr1:70818800-70820800	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr1:70818800-70820800	Active TSS	Brain Cingulate Gyrus	brain
50	chr1:70818800-70820800	Active TSS	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links