Variant report

Variant	rs2411061
Chromosome Location	chr7:102613490-102613491
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr7:102613356-102614092	K562	blood:	n/a	n/a
2	PML	chr7:102613327-102614248	K562	blood:	n/a	n/a
3	IRF1	chr7:102613315-102614134	K562	blood:	n/a	chr7:102613343-102613357
4	POLR2A	chr7:102613447-102614687	K562	blood:	n/a	n/a
5	STAT5A	chr7:102613449-102614216	K562	blood:	n/a	n/a
6	GATA2	chr7:102613323-102614105	HUVEC	blood vessel:	n/a	n/a
7	PML	chr7:102613395-102614428	K562	blood:	n/a	n/a
8	POLR2A	chr7:102613362-102614673	K562	blood:	n/a	n/a
9	POLR2A	chr7:102613412-102614067	HUVEC	blood vessel:	n/a	n/a
10	CEBPB	chr7:102613340-102614174	K562	blood:	n/a	n/a
11	POLR2A	chr7:102613188-102614671	K562	blood:	n/a	n/a
12	EP300	chr7:102613478-102614058	GM12878	blood:	n/a	n/a
13	HEY1	chr7:102613421-102614695	K562	blood:	n/a	n/a
14	POLR2A	chr7:102613349-102614031	U87	brain:	n/a	n/a
15	IRF1	chr7:102613325-102614493	K562	blood:	n/a	chr7:102613343-102613357
16	NR2F2	chr7:102613345-102616007	K562	blood:	n/a	n/a
17	TBL1XR1	chr7:102613467-102614152	K562	blood:	n/a	n/a
18	CCNT2	chr7:102613489-102613769	K562	blood:	n/a	n/a
19	CUX1	chr7:102613462-102614241	K562	blood:	n/a	n/a
20	TBP	chr7:102613469-102614434	K562	blood:	n/a	n/a
21	BCLAF1	chr7:102613400-102614259	K562	blood:	n/a	n/a
22	CBX3	chr7:102613423-102614555	K562	blood:	n/a	n/a
23	JUND	chr7:102613465-102614184	K562	blood:	n/a	n/a
24	TEAD4	chr7:102613337-102614630	K562	blood:	n/a	n/a
25	POLR2A	chr7:102613470-102614420	K562	blood:	n/a	n/a
26	NR2F2	chr7:102613475-102614365	K562	blood:	n/a	n/a
27	TRIM28	chr7:102613403-102614585	K562	blood:	n/a	n/a
28	TEAD4	chr7:102613326-102614390	K562	blood:	n/a	n/a
29	CEBPB	chr7:102613488-102614107	K562	blood:	n/a	n/a
30	POLR2A	chr7:102613452-102614495	K562	blood:	n/a	n/a
31	ELF1	chr7:102613482-102614116	K562	blood:	n/a	chr7:102613772-102613785
32	MYC	chr7:102613411-102614476	K562	blood:	n/a	n/a
33	ATF3	chr7:102613482-102614149	K562	blood:	n/a	n/a
34	JUN	chr7:102612903-102615140	K562	blood:	n/a	n/a
35	POLR2A	chr7:102613490-102614314	K562	blood:	n/a	n/a
36	POLR2A	chr7:102613095-102614654	K562	blood:	n/a	n/a
37	POLR2A	chr7:102613384-102614230	U87	brain:	n/a	n/a
38	POLR2A	chr7:102613480-102614475	K562	blood:	n/a	n/a
39	ARID3A	chr7:102613385-102614106	K562	blood:	n/a	n/a
40	GATA2	chr7:102613431-102614080	K562	blood:	n/a	n/a
41	POLR2A	chr7:102613390-102614230	U87	brain:	n/a	n/a
42	MAFF	chr7:102613417-102614021	K562	blood:	n/a	n/a
43	POLR2A	chr7:102613424-102614578	K562	blood:	n/a	n/a
44	HEY1	chr7:102613450-102614578	K562	blood:	n/a	n/a
45	RCOR1	chr7:102613465-102614354	K562	blood:	n/a	n/a
46	RFX5	chr7:102613460-102614079	K562	blood:	n/a	n/a
47	CEBPD	chr7:102613402-102614386	K562	blood:	n/a	n/a
48	POLR2A	chr7:102613487-102614160	HUVEC	blood vessel:	n/a	n/a
49	CBX3	chr7:102613428-102614115	K562	blood:	n/a	n/a
50	POLR2A	chr7:102613447-102614263	HL-60	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:102497060..102498758-chr7:102613043..102615053,2	K562	blood:
2	chr7:102613006..102614516-chr7:102715583..102717366,2	K562	blood:

No data

Variant related genes	Relation type
NFE4	TF binding region
ENSG00000170632	Chromatin interaction
ENSG00000238324	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10487281	1.00[CHB][hapmap]
rs10487284	1.00[CHB][hapmap]
rs11496066	1.00[CHB][hapmap]
rs12113073	1.00[CHB][hapmap]
rs12113233	1.00[ASN][1000 genomes]
rs12113318	0.82[YRI][hapmap]
rs12113759	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs17135875	1.00[CHB][hapmap]
rs17135913	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs17135916	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs17474893	1.00[CHB][hapmap]
rs2041094	1.00[CHB][hapmap]
rs2228687	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs4377880	1.00[CHB][hapmap]
rs4398822	1.00[CHB][hapmap]
rs4610658	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55681588	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55781834	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55825804	0.83[ASN][1000 genomes]
rs55849741	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55851590	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56146438	1.00[ASN][1000 genomes]
rs56186316	1.00[ASN][1000 genomes]
rs56314487	0.88[EUR][1000 genomes]
rs56336567	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56692051	0.88[EUR][1000 genomes]
rs6465886	1.00[CEU][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6465887	0.85[CEU][hapmap];0.82[YRI][hapmap]
rs6465889	0.83[YRI][hapmap]
rs66712128	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6955064	0.90[EUR][1000 genomes]
rs6964296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs6965463	0.83[CEU][hapmap];0.80[YRI][hapmap]
rs6968036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs727175	1.00[CHB][hapmap]
rs73192019	0.89[EUR][1000 genomes]
rs73192025	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192026	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73714541	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7777217	0.83[CEU][hapmap];0.80[YRI][hapmap]
rs7779854	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs7781557	1.00[CHB][hapmap]
rs7790451	1.00[ASN][1000 genomes]
rs7797873	1.00[ASN][1000 genomes]
rs7798582	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7809047	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv464667	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv608060	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv5881	chr7:102610488-102655699	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2411061	LRRC17	cis	Stomach	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102591000-102619400	Weak transcription	HSMM	muscle
2	chr7:102608800-102618600	Weak transcription	Osteobl	bone
3	chr7:102611800-102615000	Active TSS	K562	blood
4	chr7:102612400-102613600	Active TSS	Primary B cells from cord blood	blood
5	chr7:102612600-102613800	Flanking Active TSS	HUVEC	blood vessel
6	chr7:102613000-102625600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:102613200-102631200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:102613400-102613600	Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr7:102613400-102613800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links