Variant report

Variant	rs10129316
Chromosome Location	chr14:67959100-67959101
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	MXI1	chr14:67958379-67959603	SK-N-SH	brain:	n/a	chr14:67958773-67958782
2	GATA2	chr14:67958612-67959339	SH-SY5Y	brain:	n/a	n/a
3	REST	chr14:67958713-67959214	PFSK-1	brain:	n/a	chr14:67958976-67958985
4	REST	chr14:67958820-67959158	SK-N-SH	brain:	n/a	chr14:67958976-67958985
5	REST	chr14:67958711-67959179	PFSK-1	brain:	n/a	chr14:67958976-67958985
6	MXI1	chr14:67958917-67959251	H1-hESC	embryonic stem cell:	n/a	n/a
7	REST	chr14:67958752-67959163	SK-N-SH	brain:	n/a	chr14:67958976-67958985
8	REST	chr14:67958791-67959108	ECC-1	luminal epithelium:	n/a	chr14:67958976-67958985
9	REST	chr14:67958682-67959238	H1-hESC	embryonic stem cell:	n/a	chr14:67958976-67958985
10	ZNF143	chr14:67958903-67959162	H1-hESC	embryonic stem cell:	n/a	n/a
11	ESR1	chr14:67959069-67959444	T-47D	breast:	n/a	n/a
12	REST	chr14:67958829-67959123	Hela-S3	cervix:	n/a	chr14:67958976-67958985
13	SIN3A	chr14:67958893-67959126	H1-hESC	embryonic stem cell:	n/a	chr14:67958978-67958986 chr14:67959099-67959110
14	EP300	chr14:67958854-67959128	SK-N-SH_RA	brain:	n/a	n/a
15	EP300	chr14:67958207-67959403	SK-N-SH	brain:	n/a	n/a
16	REST	chr14:67958816-67959100	PFSK-1	brain:	n/a	chr14:67958976-67958985
17	REST	chr14:67958779-67959204	MCF-7	breast:	n/a	chr14:67958976-67958985
18	REST	chr14:67958809-67959141	H1-hESC	embryonic stem cell:	n/a	chr14:67958976-67958985

No.	Distal block	Cell Line	Cell type
1	chr14:67946842..67948505-chr14:67958854..67960376,2	MCF-7	breast:
2	chr14:67958532..67960462-chr14:67983895..67986078,2	MCF-7	breast:
3	chr14:67953372..67955912-chr14:67957756..67960248,2	K562	blood:

Variant related genes	Relation type
TMEM229B	TF binding region
ENSG00000198133	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs61988187	1.00[ASN][1000 genomes]
rs61988217	1.00[ASN][1000 genomes]
rs7149727	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	nsv1045518	chr14:67529049-67959582	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1035855	chr14:67935684-67964355	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1320	chr14:67938724-67984157	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10129316	FNTB	cis	cerebellum	SCAN
rs10129316	ACTN1	cis	cerebellum	SCAN
rs10129316	PPP2R5E	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:67935000-67977200	Weak transcription	Brain Angular Gyrus	brain
2	chr14:67955800-67959600	Enhancers	Primary B cells from peripheral blood	blood
3	chr14:67955800-67959600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr14:67956000-67959600	Enhancers	Primary B cells from cord blood	blood
5	chr14:67956000-67978000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr14:67956200-67959200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr14:67956200-67959400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr14:67956200-67960200	Weak transcription	Primary T cells from cord blood	blood
9	chr14:67956200-67981000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr14:67956400-67959200	Weak transcription	Dnd41	blood
11	chr14:67956400-67960400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr14:67956800-67961000	ZNF genes & repeats	GM12878-XiMat	blood
13	chr14:67957000-67959200	Enhancers	H9 Cell Line	embryonic stem cell
14	chr14:67957200-67960000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr14:67957400-67959400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr14:67957600-67959400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr14:67957600-67959400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr14:67957600-67959400	Enhancers	Fetal Stomach	stomach
19	chr14:67957800-67959200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr14:67957800-67959200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr14:67957800-67959400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr14:67958000-67959400	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr14:67958200-67959400	Enhancers	Fetal Brain Male	brain
24	chr14:67958200-67959400	Enhancers	Pancreas	Pancrea
25	chr14:67958400-67959400	Enhancers	Brain Germinal Matrix	brain
26	chr14:67958600-67959200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr14:67958600-67959200	Enhancers	Fetal Muscle Leg	muscle
28	chr14:67958600-67959400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr14:67958600-67959400	Enhancers	Fetal Brain Female	brain
30	chr14:67958800-67959200	Enhancers	Brain Cingulate Gyrus	brain
31	chr14:67958800-67959400	Enhancers	Fetal Intestine Large	intestine
32	chr14:67958800-67959400	Enhancers	Fetal Muscle Trunk	muscle
33	chr14:67958800-67959400	Enhancers	Left Ventricle	heart
34	chr14:67959000-67959200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr14:67959000-67959400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr14:67959000-67959400	Enhancers	Spleen	Spleen
37	chr14:67959000-67959600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr14:67959000-67960000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr14:67959000-67961600	ZNF genes & repeats	Fetal Intestine Small	intestine

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