Variant report

Variant	rs615205
Chromosome Location	chr11:66337987-66337988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr11:66337667-66338502	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr11:66337670-66338270	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr11:66337627-66338800	H1-neurons	neurons:	n/a	n/a
4	POLR2A	chr11:66337703-66338488	H1-neurons	neurons:	n/a	n/a
5	CEBPB	chr11:66337965-66338067	IMR90	lung:	n/a	n/a
6	TAF1	chr11:66337910-66338421	H1-neurons	neurons:	n/a	n/a
7	CEBPB	chr11:66337969-66338034	A549	lung:	n/a	n/a
8	CEBPB	chr11:66337842-66338144	HepG2	liver:	n/a	n/a
9	TAF1	chr11:66337674-66338365	H1-hESC	embryonic stem cell:	n/a	n/a
10	TEAD4	chr11:66337552-66338340	H1-hESC	embryonic stem cell:	n/a	n/a
11	CEBPB	chr11:66337973-66338003	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr11:66337714-66338422	H1-hESC	embryonic stem cell:	n/a	n/a
13	TBP	chr11:66337668-66338316	H1-hESC	embryonic stem cell:	n/a	n/a
14	TEAD4	chr11:66337580-66338349	H1-hESC	embryonic stem cell:	n/a	n/a
15	CEBPB	chr11:66337601-66338315	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr11:66337807-66338470	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr11:66337436-66338802	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66311475..66316022-chr11:66335981..66338223,4	MCF-7	breast:

No data

Variant related genes	Relation type
CTSF	TF binding region
ENSG00000248746	Chromatin interaction
ENSG00000174165	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10736656	0.84[ASN][1000 genomes]
rs10791882	0.93[ASN][1000 genomes]
rs1127894	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1671062	0.84[ASN][1000 genomes]
rs1671063	0.82[ASN][1000 genomes]
rs1671064	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1671065	0.84[ASN][1000 genomes]
rs1700189	0.82[ASN][1000 genomes]
rs1791684	0.82[ASN][1000 genomes]
rs1791686	0.86[ASN][1000 genomes]
rs1815739	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2000939	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3018318	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs486584	0.92[ASN][1000 genomes]
rs503250	0.80[ASN][1000 genomes]
rs509556	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs531490	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs540874	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs545009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs556759	0.80[ASN][1000 genomes]
rs560556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs618838	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs630021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs662094	0.83[AFR][1000 genomes]
rs677488	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs678397	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8432	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
4	nsv897787	chr11:66300348-66347850	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv897788	chr11:66319262-66347850	Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs615205	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs615205	ACTN3	cis	Muscle Skeletal	GTEx
rs615205	CCS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66336200-66338400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:66336400-66338000	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr11:66336400-66338000	Weak transcription	Fetal Kidney	kidney
4	chr11:66336400-66346600	Weak transcription	Right Atrium	heart
5	chr11:66336800-66338800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr11:66336800-66338800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr11:66336800-66338800	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr11:66337000-66338000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr11:66337000-66346600	Weak transcription	K562	blood
10	chr11:66337400-66338400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:66337600-66338000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr11:66337600-66338200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr11:66337600-66338600	Enhancers	H9 Cell Line	embryonic stem cell
14	chr11:66337600-66338600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr11:66337600-66338600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr11:66337600-66338600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:66337600-66338800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:66337600-66338800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:66337600-66338800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:66337600-66338800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr11:66337800-66338000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:66337800-66338000	Enhancers	Ovary	ovary
23	chr11:66337800-66338000	Bivalent Enhancer	HepG2	liver
24	chr11:66337800-66338200	Enhancers	HSMMtube	muscle
25	chr11:66337800-66338400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr11:66337800-66338600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:66337800-66338600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:66337800-66338800	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr11:66337800-66338800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr11:66337800-66338800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links