Variant report

Variant	rs2218994
Chromosome Location	chr14:64969225-64969226
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	GATA3	chr14:64967678-64969343	SK-N-SH	brain:	n/a	chr14:64968270-64968277 chr14:64968712-64968720 chr14:64968230-64968240 chr14:64968534-64968542 chr14:64968270-64968277 chr14:64968265-64968281 chr14:64968270-64968277
2	POLR2A	chr14:64968377-64972910	GM12878	blood:	n/a	n/a
3	BRCA1	chr14:64968189-64969581	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr14:64968214-64972761	Hela-S3	cervix:	n/a	n/a
5	CHD2	chr14:64968982-64969405	GM12878	blood:	n/a	n/a
6	GATA3	chr14:64968252-64969301	SH-SY5Y	brain:	n/a	chr14:64968270-64968277 chr14:64968712-64968720 chr14:64968534-64968542 chr14:64968270-64968277 chr14:64968265-64968281 chr14:64968270-64968277
7	MEF2A	chr14:64969103-64969515	GM12878	blood:	n/a	chr14:64969259-64969273
8	WRNIP1	chr14:64968374-64970318	GM12878	blood:	n/a	n/a
9	POLR2A	chr14:64969191-64969698	U87	brain:	n/a	n/a
10	CEBPB	chr14:64969033-64969704	GM12878	blood:	n/a	n/a
11	POLR2A	chr14:64968195-64972949	GM12891	blood:	n/a	n/a
12	CHD1	chr14:64967702-64973034	IMR90	lung:	n/a	chr14:64971962-64971972
13	RUNX3	chr14:64968889-64969563	GM12878	blood:	n/a	n/a
14	HCFC1	chr14:64967718-64972649	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr14:64969149-64972818	GM12892	blood:	n/a	n/a
16	CTCF	chr14:64969080-64969230	GM06990	blood:	n/a	n/a
17	CTCF	chr14:64969180-64969330	GM12872	blood:	n/a	n/a
18	GATA2	chr14:64968274-64969291	SH-SY5Y	brain:	n/a	chr14:64968534-64968542
19	POLR2A	chr14:64969150-64969587	ECC-1	luminal epithelium:	n/a	n/a
20	STAT1	chr14:64969191-64969681	GM12878	blood:	n/a	n/a
21	POLR2A	chr14:64968431-64972911	IMR90	lung:	n/a	n/a
22	MXI1	chr14:64969166-64972760	GM12878	blood:	n/a	chr14:64970522-64970531
23	POLR2A	chr14:64967953-64972968	GM12878	blood:	n/a	n/a
24	RELA	chr14:64968247-64972684	GM12891	blood:	n/a	chr14:64970754-64970763 chr14:64970754-64970763
25	RAD21	chr14:64969127-64969695	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr14:64969160-64969310	GM12872	blood:	n/a	n/a
27	CTCF	chr14:64969140-64969290	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr14:64969135-64972858	SK-N-MC	brain:	n/a	n/a
29	STAT3	chr14:64967976-64969293	MCF10A-Er-Src	breast:	n/a	chr14:64968445-64968456
30	POLR2A	chr14:64968671-64972652	Raji	blood:	n/a	n/a
31	MYC	chr14:64969065-64969228	MCF10A-Er-Src	breast:	n/a	n/a
32	CTCF	chr14:64969089-64969440	GM12878	blood:	n/a	n/a
33	CTCF	chr14:64969209-64969323	GM10248	blood:	n/a	n/a
34	CTCF	chr14:64969220-64969370	HMEC	breast:	n/a	n/a
35	MTA3	chr14:64968159-64972791	GM12878	blood:	n/a	n/a
36	CTCF	chr14:64969160-64969310	GM12874	blood:	n/a	n/a
37	EP300	chr14:64967668-64973008	SK-N-SH	brain:	n/a	chr14:64970348-64970364 chr14:64972052-64972068 chr14:64970498-64970507 chr14:64970293-64970309 chr14:64972041-64972057 chr14:64970131-64970147
38	CTCF	chr14:64969180-64969330	HMEC	breast:	n/a	n/a
39	CTCF	chr14:64969180-64969330	GM12878	blood:	n/a	n/a
40	CTCF	chr14:64969140-64969290	GM12873	blood:	n/a	n/a
41	CTCF	chr14:64969220-64969370	GM12873	blood:	n/a	n/a
42	GATA1	chr14:64969219-64970811	PBDE	blood:	n/a	n/a
43	EP300	chr14:64969146-64969434	GM12878	blood:	n/a	n/a
44	TBL1XR1	chr14:64968872-64969441	GM12878	blood:	n/a	n/a
45	STAT3	chr14:64967964-64969294	MCF10A-Er-Src	breast:	n/a	chr14:64968445-64968456
46	MAX	chr14:64969174-64972770	A549	lung:	n/a	chr14:64970856-64970866 chr14:64970521-64970530 chr14:64970529-64970536 chr14:64970741-64970748 chr14:64970519-64970528 chr14:64970520-64970531 chr14:64971960-64971970
47	ZNF143	chr14:64969110-64969668	GM12878	blood:	n/a	chr14:64969233-64969251
48	POLR2A	chr14:64968330-64972692	GM18505	blood:	n/a	n/a
49	SMC3	chr14:64969071-64969416	Hela-S3	cervix:	n/a	n/a
50	RAD21	chr14:64969085-64969383	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:64853586..64859592-chr14:64968792..64973445,7	MCF-7	breast:
2	chr14:64969034..64974113-chr14:65005478..65010690,22	MCF-7	breast:
3	chr14:64969193..64971407-chr14:65001217..65003397,2	K562	blood:
4	chr14:64906156..64910833-chr14:64968657..64972449,4	MCF-7	breast:
5	chr14:64969038..64970708-chr17:41464900..41467656,2	MCF-7	breast:
6	chr14:64950027..64951532-chr14:64966808..64969556,2	MCF-7	breast:
7	chr14:64969164..64972149-chr14:65189834..65193113,3	MCF-7	breast:
8	chr14:64968342..64970352-chr14:65235886..65238559,2	MCF-7	breast:
9	chr14:64967118..64970041-chr14:65086433..65088107,2	MCF-7	breast:
10	chr14:64799661..64807761-chr14:64967157..64973754,20	MCF-7	breast:
11	chr14:64969208..64970708-chr17:41380727..41383281,2	K562	blood:
12	chr14:64969208..64970728-chr17:41380300..41382227,2	K562	blood:
13	chr14:64853142..64856847-chr14:64968558..64973163,8	K562	blood:
14	chr14:64968319..64971699-chr14:65168654..65172546,5	MCF-7	breast:
15	chr14:64803146..64808978-chr14:64966714..64972227,18	MCF-7	breast:
16	chr14:64803252..64809099-chr14:64968512..64973071,12	K562	blood:
17	chr14:64930987..64933079-chr14:64967526..64973126,5	K562	blood:
18	chr14:64930505..64934030-chr14:64968774..64972974,8	MCF-7	breast:
19	chr14:64967941..64976890-chr14:65001097..65012463,31	MCF-7	breast:
20	chr14:64968210..64972351-chr14:65168934..65172584,5	MCF-7	breast:

Variant related genes	Relation type
ZBTB1	TF binding region
ENSG00000179841	Chromatin interaction
ENSG00000259116	Chromatin interaction
ENSG00000214770	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000236383	Chromatin interaction
ENSG00000259160	Chromatin interaction
ENSG00000272909	Chromatin interaction
ENSG00000140009	Chromatin interaction
ENSG00000126822	Chromatin interaction
ENSG00000126803	Chromatin interaction
ENSG00000100714	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10138919	0.85[EUR][1000 genomes]
rs1040612	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs10431708	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10498515	0.88[CEU][hapmap]
rs1063391	0.85[CHB][hapmap];0.80[CHD][hapmap]
rs11158546	0.82[EUR][1000 genomes]
rs12432891	0.85[CHB][hapmap];0.80[CHD][hapmap]
rs1256146	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]
rs1256148	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.85[EUR][1000 genomes]
rs1256150	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12589322	0.88[CEU][hapmap]
rs12886478	0.84[AFR][1000 genomes]
rs12894050	0.84[EUR][1000 genomes]
rs12894807	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs1453005	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1901737	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2038270	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2045022	0.85[CHB][hapmap];0.80[CHD][hapmap]
rs2602156	0.80[AFR][1000 genomes]
rs34616731	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35872489	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4313734	0.85[CHB][hapmap];0.80[CHD][hapmap]
rs4902287	0.97[AMR][1000 genomes]
rs4902288	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902295	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs4902296	0.85[EUR][1000 genomes]
rs4902297	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs4902298	0.85[EUR][1000 genomes]
rs4902299	0.81[ASW][hapmap]
rs7145155	0.85[CHB][hapmap]
rs7148289	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs7149152	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7151628	0.85[CHB][hapmap]
rs7156953	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7159809	0.88[CEU][hapmap]
rs761547	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs8007313	0.84[MEX][hapmap]
rs8011038	0.85[CHB][hapmap]
rs8016170	0.85[EUR][1000 genomes]
rs8016361	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8017407	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs8018169	0.85[EUR][1000 genomes]
rs8022447	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs926802	0.88[CEU][hapmap]
rs9671381	0.87[CEU][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2218994	PLEKHG3	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64954800-64969600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:64961200-64969600	Weak transcription	Ovary	ovary
3	chr14:64966400-64969600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr14:64967200-64969800	Flanking Active TSS	Dnd41	blood
5	chr14:64967400-64969800	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr14:64967800-64969600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr14:64967800-64969600	Flanking Active TSS	Liver	Liver
8	chr14:64967800-64969800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr14:64967800-64970200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr14:64967800-64974200	Active TSS	GM12878-XiMat	blood
11	chr14:64968000-64969400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr14:64968000-64969400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr14:64968000-64969400	Enhancers	Stomach Mucosa	stomach
14	chr14:64968000-64969400	Flanking Active TSS	A549	lung
15	chr14:64968000-64969400	Enhancers	K562	blood
16	chr14:64968000-64969600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr14:64968000-64969600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr14:64968000-64969600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr14:64968000-64969600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr14:64968000-64969600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr14:64968000-64969600	Flanking Active TSS	Hela-S3	cervix
22	chr14:64968000-64969800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr14:64968000-64969800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr14:64968000-64969800	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr14:64968000-64969800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr14:64968000-64969800	Flanking Active TSS	Osteobl	bone
27	chr14:64968000-64970000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr14:64968000-64970200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr14:64968000-64970400	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr14:64968000-64973400	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr14:64968200-64969400	Flanking Active TSS	HepG2	liver
32	chr14:64968200-64969400	Enhancers	NH-A	brain
33	chr14:64968200-64969600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr14:64968200-64969600	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr14:64968200-64969600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr14:64968200-64969600	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr14:64968200-64969600	Flanking Active TSS	Fetal Thymus	thymus
38	chr14:64968200-64969600	Enhancers	Placenta Amnion	Placenta Amnion
39	chr14:64968200-64969600	Flanking Active TSS	HMEC	breast
40	chr14:64968200-64969600	Flanking Active TSS	NHDF-Ad	bronchial
41	chr14:64968200-64969600	Flanking Active TSS	NHEK	skin
42	chr14:64968200-64969800	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr14:64968200-64969800	Flanking Active TSS	Rectal Smooth Muscle	rectum
44	chr14:64968200-64969800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr14:64968200-64969800	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr14:64968200-64970000	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr14:64968200-64970000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr14:64968200-64970200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr14:64968200-64970200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr14:64968200-64970400	Flanking Active TSS	Primary hematopoietic stem cells	blood

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