Variant report

Variant	rs1200114
Chromosome Location	chr1:169060489-169060490
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	POLR2A	chr1:169060073-169060958	GM12892	blood:	n/a	n/a
2	EP300	chr1:169060128-169060960	GM12878	blood:	n/a	chr1:169060759-169060773
3	FOXM1	chr1:169059475-169061034	GM12878	blood:	n/a	n/a
4	WRNIP1	chr1:169060093-169061300	GM12878	blood:	n/a	n/a
5	EP300	chr1:169059581-169060969	GM12878	blood:	n/a	chr1:169060062-169060076 chr1:169060759-169060773
6	FOXM1	chr1:169060072-169060958	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:169060025-169061098	GM12892	blood:	n/a	n/a
8	NFIC	chr1:169059890-169060997	GM12878	blood:	n/a	n/a
9	YY1	chr1:169060233-169061112	GM12878	blood:	n/a	n/a
10	SPI1	chr1:169060352-169061115	GM12878	blood:	n/a	chr1:169060758-169060771 chr1:169060764-169060773 chr1:169060760-169060769
11	IRF4	chr1:169060193-169061062	GM12878	blood:	n/a	n/a
12	NFIC	chr1:169059455-169061130	GM12878	blood:	n/a	chr1:169059744-169059772
13	POLR2A	chr1:169060145-169060859	GM12892	blood:	n/a	n/a
14	RUNX3	chr1:169059509-169061091	GM12878	blood:	n/a	n/a
15	BATF	chr1:169059502-169061064	GM12878	blood:	n/a	n/a
16	ATF2	chr1:169060229-169061108	GM12878	blood:	n/a	n/a
17	EBF1	chr1:169059636-169060996	GM12878	blood:	n/a	chr1:169060243-169060254
18	YY1	chr1:169060407-169061087	K562	blood:	n/a	n/a
19	MTA3	chr1:169059519-169061164	GM12878	blood:	n/a	n/a
20	YY1	chr1:169060058-169060577	GM12892	blood:	n/a	chr1:169060131-169060139
21	PML	chr1:169060111-169061040	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:169060123-169061021	GM12892	blood:	n/a	n/a
23	YY1	chr1:169060066-169060590	GM12878	blood:	n/a	chr1:169060131-169060139
24	RELA	chr1:169059637-169061232	GM19099	blood:	n/a	n/a
25	ATF2	chr1:169059553-169061092	GM12878	blood:	n/a	n/a
26	MTA3	chr1:169060076-169060955	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169058922..169062044-chr1:169078409..169081693,3	K562	blood:
2	chr1:169055830..169060702-chr1:169073415..169077056,5	MCF-7	breast:
3	chr1:169053133..169065213-chr1:169070028..169077898,15	MCF-7	breast:

Variant related genes	Relation type
LINC00970	TF binding region
ENSG00000237707	Chromatin interaction
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1040506	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1200089	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1200092	0.86[EUR][1000 genomes]
rs1200097	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1200099	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1200103	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1200105	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1200106	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1200108	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs1200115	0.96[CEU][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1200122	0.91[AMR][1000 genomes]
rs1200125	0.93[AMR][1000 genomes]
rs1200128	0.93[AMR][1000 genomes]
rs1200132	1.00[CHB][hapmap]
rs1575041	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1575042	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2982459	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2982461	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3007369	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3007370	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4656175	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs932393	0.91[AMR][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	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats 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 lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169055200-169062200	Enhancers	Brain Anterior Caudate	brain
2	chr1:169056200-169062600	Enhancers	Brain Inferior Temporal Lobe	brain
3	chr1:169056400-169062800	Enhancers	Brain Cingulate Gyrus	brain
4	chr1:169056600-169063400	Enhancers	Brain Hippocampus Middle	brain
5	chr1:169056800-169064000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:169057200-169064000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:169058800-169064600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:169059400-169061400	Flanking Active TSS	GM12878-XiMat	blood
9	chr1:169059600-169062200	Enhancers	Brain Angular Gyrus	brain
10	chr1:169059800-169060800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:169059800-169062000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:169060000-169064400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:169060200-169061000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:169060400-169060600	Flanking Active TSS	Brain Substantia Nigra	brain
15	chr1:169060400-169060600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr1:169060400-169068000	Weak transcription	Fetal Heart	heart

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