Variant report

Variant	rs1256146
Chromosome Location	chr14:64920665-64920666
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	chr14:64920488-64920688	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:64918310..64922464-chr14:64924231..64927015,4	K562	blood:
2	chr14:64910448..64911970-chr14:64919043..64921464,2	K562	blood:
3	chr14:64919296..64921199-chr14:64925016..64927012,2	MCF-7	breast:

Variant related genes	Relation type
MTHFD1	TF binding region
ENSG00000100714	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10138919	0.81[EUR][1000 genomes]
rs1040612	0.88[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs10431708	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10498515	0.88[CEU][hapmap]
rs1063391	0.85[CHB][hapmap]
rs11158546	0.80[EUR][1000 genomes]
rs12432891	0.85[CHB][hapmap]
rs1256140	0.81[AMR][1000 genomes]
rs1256141	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1256148	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1256150	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12589322	0.88[CEU][hapmap]
rs12886478	0.90[AFR][1000 genomes]
rs12894050	0.81[EUR][1000 genomes]
rs12894807	0.83[CEU][hapmap]
rs1453005	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1901737	0.83[AMR][1000 genomes]
rs2038270	0.88[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs2045022	0.85[CHB][hapmap]
rs2218994	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2602156	0.85[AFR][1000 genomes]
rs34616731	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35262226	0.83[AFR][1000 genomes]
rs35872489	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4313734	0.85[CHB][hapmap]
rs45558338	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4902287	0.83[AMR][1000 genomes]
rs4902288	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4902295	0.88[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs4902296	0.82[EUR][1000 genomes]
rs4902297	0.88[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs4902298	0.82[EUR][1000 genomes]
rs4902299	0.82[ASW][hapmap]
rs7145155	0.85[CHB][hapmap]
rs7148289	0.88[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs7149152	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes]
rs7151628	0.85[CHB][hapmap]
rs7156953	1.00[CEU][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.90[EUR][1000 genomes]
rs7159809	0.88[CEU][hapmap]
rs761547	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs8007313	0.83[MEX][hapmap]
rs8011038	0.85[CHB][hapmap]
rs8016170	0.82[EUR][1000 genomes]
rs8016361	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes]
rs8017407	0.88[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs8018169	0.82[EUR][1000 genomes]
rs8022447	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs926802	0.88[CEU][hapmap]
rs9671381	0.87[CEU][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1256146	PLEKHG3	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64856200-64931200	Weak transcription	Stomach Mucosa	stomach
2	chr14:64861800-64931600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:64867200-64927000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr14:64867200-64929600	Strong transcription	Dnd41	blood
5	chr14:64874000-64928400	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr14:64877000-64927000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr14:64877000-64929400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr14:64877400-64928200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr14:64877800-64929200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr14:64878200-64921200	Strong transcription	Liver	Liver
11	chr14:64881600-64929000	Strong transcription	Fetal Thymus	thymus
12	chr14:64888000-64923000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr14:64891200-64928600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr14:64900400-64931800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr14:64905800-64931400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr14:64907800-64921400	Weak transcription	Fetal Brain Male	brain
17	chr14:64909400-64921200	Weak transcription	Right Ventricle	heart
18	chr14:64910600-64931200	Weak transcription	Fetal Heart	heart
19	chr14:64911200-64921200	Weak transcription	Colonic Mucosa	Colon
20	chr14:64911200-64931400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr14:64911800-64931400	Weak transcription	Colon Smooth Muscle	Colon
22	chr14:64912200-64929600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr14:64912400-64923600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr14:64912400-64925000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr14:64912400-64930200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:64912600-64923400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr14:64912600-64926800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr14:64912600-64929600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr14:64913200-64923200	Strong transcription	Fetal Intestine Small	intestine
30	chr14:64913400-64929600	Strong transcription	Fetal Stomach	stomach
31	chr14:64913600-64929000	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr14:64913600-64929200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr14:64913800-64931200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr14:64914200-64922600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr14:64914200-64924000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr14:64914200-64924200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr14:64914200-64927200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr14:64914200-64927400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr14:64914400-64921600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr14:64914400-64922600	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr14:64914400-64923400	Strong transcription	Osteobl	bone
42	chr14:64914400-64924600	Strong transcription	Adipose Nuclei	Adipose
43	chr14:64914400-64925000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr14:64914400-64926400	Strong transcription	A549	lung
45	chr14:64914400-64927000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr14:64914400-64927000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr14:64914600-64923400	Strong transcription	Left Ventricle	heart
48	chr14:64914800-64922600	Strong transcription	Brain Hippocampus Middle	brain
49	chr14:64914800-64923200	Strong transcription	Thymus	Thymus
50	chr14:64914800-64924200	Strong transcription	Duodenum Mucosa	Duodenum

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