Variant report

Variant	rs2655997
Chromosome Location	chr14:77670489-77670490
allele	C/T
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	GATA2	chr14:77670414-77670956	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr14:77670243-77670856	SH-SY5Y	brain:	n/a	chr14:77670248-77670255
3	NR2F2	chr14:77670138-77671235	MCF-7	breast:	n/a	n/a
4	MXI1	chr14:77669821-77670978	SK-N-SH	brain:	n/a	chr14:77670475-77670490
5	CEBPB	chr14:77670262-77671146	MCF-7	breast:	n/a	n/a
6	POLR2A	chr14:77670305-77670727	H1-neurons	neurons:	n/a	n/a
7	SIN3AK20	chr14:77670197-77671163	MCF-7	breast:	n/a	n/a
8	GATA3	chr14:77670203-77671302	MCF-7	breast:	n/a	chr14:77670248-77670255
9	GATA3	chr14:77670381-77671337	MCF-7	breast:	n/a	n/a
10	GATA3	chr14:77670465-77671054	MCF-7	breast:	n/a	n/a
11	NR2F2	chr14:77670416-77671220	MCF-7	breast:	n/a	n/a
12	SIN3AK20	chr14:77670139-77671477	MCF-7	breast:	n/a	n/a
13	POLR2A	chr14:77670082-77670614	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:77669395..77671250-chr14:77783516..77785944,2	MCF-7	breast:
2	chr14:77670339..77672949-chr14:77673873..77676008,3	MCF-7	breast:
3	chr14:77669292..77670874-chr14:77786731..77788343,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201384	TF binding region
ENSG00000009830	Chromatin interaction
ENSG00000100577	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1078692	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs11159251	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs11627977	0.84[YRI][hapmap]
rs12881255	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs12891631	1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs12896627	0.96[ASN][1000 genomes]
rs1467011	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1504521	0.91[ASN][1000 genomes]
rs17105457	0.95[ASN][1000 genomes]
rs1848402	0.90[ASN][1000 genomes]
rs1861420	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs207802	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs207804	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2655996	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2661828	0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs4021320	0.81[JPT][hapmap]
rs4021325	1.00[ASN][1000 genomes]
rs4313745	0.85[CEU][hapmap]
rs70165	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs7140198	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7148579	0.88[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs7154702	0.82[ASN][1000 genomes]
rs7155226	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8014837	0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs8018250	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs888064	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431017	chr14:76938089-77854647	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv832834	chr14:77554987-77724357	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2655997	YLPM1	cis	cerebellum	SCAN
rs2655997	C14orf178	cis	parietal	SCAN
rs2655997	VSX2	cis	parietal	SCAN
rs2655997	ADCK1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77654200-77709400	Weak transcription	Esophagus	oesophagus
2	chr14:77654600-77679400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr14:77662000-77674400	Weak transcription	Brain Substantia Nigra	brain
4	chr14:77662800-77671600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr14:77667800-77671200	Enhancers	Fetal Brain Male	brain
6	chr14:77668600-77671000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr14:77669800-77670800	Enhancers	Brain Anterior Caudate	brain
8	chr14:77669800-77670800	Enhancers	Brain Hippocampus Middle	brain
9	chr14:77669800-77670800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr14:77669800-77671000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr14:77669800-77671000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr14:77669800-77671000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr14:77669800-77671200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr14:77669800-77671200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr14:77669800-77671200	Enhancers	Brain Cingulate Gyrus	brain
16	chr14:77669800-77671200	Enhancers	Fetal Brain Female	brain
17	chr14:77670000-77670600	Enhancers	Brain Angular Gyrus	brain
18	chr14:77670000-77670800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr14:77670000-77670800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr14:77670000-77670800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr14:77670000-77671000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr14:77670200-77670600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr14:77670200-77670800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr14:77670200-77671000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr14:77670200-77671000	Enhancers	Brain Germinal Matrix	brain
26	chr14:77670200-77671000	Bivalent Enhancer	Fetal Stomach	stomach
27	chr14:77670400-77670600	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr14:77670400-77671200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr14:77670400-77672000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr14:77670400-77672200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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