Variant report

Variant	rs35287494
Chromosome Location	chr14:64985188-64985189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64803770..64805350-chr14:64982942..64985236,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZBTB25-3	chr14:64985075-64985256	ENSG00000259116.1
2	lnc-ZBTB25-3	chr14:64985075-64985256	NR_110550

Variant related genes	Relation type
ENSG00000140009	Chromatin interaction
ENSG00000214770	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10498514	1.00[JPT][hapmap]
rs10891	0.93[ASN][1000 genomes]
rs11158553	1.00[CHB][hapmap]
rs11158556	1.00[CHB][hapmap]
rs11620680	1.00[CHB][hapmap]
rs11848452	0.88[LWK][hapmap]
rs17101851	1.00[JPT][hapmap]
rs17101919	0.88[LWK][hapmap]
rs17767074	1.00[CHB][hapmap]
rs17824827	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap]
rs2295638	1.00[JPT][hapmap]
rs2295639	1.00[JPT][hapmap]
rs35062852	0.88[LWK][hapmap]
rs3818239	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs57503834	0.87[EUR][1000 genomes]
rs58644746	0.93[ASN][1000 genomes]
rs723594	1.00[CHB][hapmap];0.87[YRI][hapmap]
rs727757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74056445	0.93[ASN][1000 genomes]
rs8007506	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521823	chr14:64969342-64995694	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs35287494	MTHFD1	cis	cerebellum	SCAN
rs35287494	SPTB	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64972800-64988400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr14:64972800-64991600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:64973200-64987800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr14:64974400-64988200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr14:64974400-64988400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr14:64974800-64988600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr14:64974800-64999400	Weak transcription	Fetal Brain Male	brain
8	chr14:64974800-65006000	Weak transcription	Ovary	ovary
9	chr14:64975000-64988400	Weak transcription	HSMMtube	muscle
10	chr14:64975200-64987600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr14:64975200-64988200	Weak transcription	Fetal Muscle Leg	muscle
12	chr14:64975200-64988600	Weak transcription	Fetal Stomach	stomach
13	chr14:64976000-64988400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr14:64976000-64995400	Weak transcription	Gastric	stomach
15	chr14:64976000-64996600	Weak transcription	Esophagus	oesophagus
16	chr14:64976000-65006000	Weak transcription	Brain Germinal Matrix	brain
17	chr14:64976200-64988200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr14:64976200-64988200	Weak transcription	Fetal Intestine Large	intestine
19	chr14:64976200-64988200	Weak transcription	Placenta	Placenta
20	chr14:64976200-64988600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr14:64976200-64991800	Weak transcription	Stomach Mucosa	stomach
22	chr14:64977600-64988200	Weak transcription	Right Ventricle	heart
23	chr14:64977800-64988400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr14:64977800-64991600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr14:64977800-64992200	Weak transcription	Colonic Mucosa	Colon
26	chr14:64977800-64993600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr14:64978000-64986400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr14:64978000-64987600	Weak transcription	Fetal Intestine Small	intestine
29	chr14:64978000-64987600	Weak transcription	Thymus	Thymus
30	chr14:64978000-64988600	Weak transcription	Fetal Kidney	kidney
31	chr14:64978200-64986200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr14:64978200-64987800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr14:64978200-64988200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr14:64978200-64988200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr14:64978200-64988400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr14:64978200-64988400	Weak transcription	Fetal Lung	lung
37	chr14:64978200-64989400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:64978200-65006000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr14:64978400-64986600	Weak transcription	HUVEC	blood vessel
40	chr14:64978400-64988400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr14:64978400-64988400	Weak transcription	HepG2	liver
42	chr14:64978400-64988600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr14:64978400-64992200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr14:64978400-64992600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr14:64978600-64988200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr14:64978600-64996200	Weak transcription	Brain Angular Gyrus	brain
47	chr14:64978800-64987600	Weak transcription	Fetal Thymus	thymus
48	chr14:64978800-64987600	Weak transcription	NHEK	skin
49	chr14:64978800-64988200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr14:64979000-64987600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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