Variant report

Variant	rs229619
Chromosome Location	chr14:65290246-65290247
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	EBF1	chr14:65290071-65290311	GM12878	blood:	n/a	chr14:65290197-65290208
2	CTCF	chr14:65289940-65290270	Spleen_OC	spleen:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
3	CTCF	chr14:65289953-65290258	GM10266	blood:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
4	CREB1	chr14:65289882-65290278	A549	lung:	n/a	n/a
5	SMC3	chr14:65289899-65290394	Hela-S3	cervix:	n/a	chr14:65290112-65290126
6	MXI1	chr14:65289461-65290642	SK-N-SH	brain:	n/a	n/a
7	ZNF143	chr14:65290024-65290294	Hela-S3	cervix:	n/a	n/a
8	SMC3	chr14:65288652-65290690	SK-N-SH	brain:	n/a	chr14:65289317-65289325 chr14:65289431-65289441 chr14:65290112-65290126 chr14:65290390-65290397
9	RAD21	chr14:65289765-65290683	SK-N-SH	brain:	n/a	chr14:65290112-65290126 chr14:65290395-65290408 chr14:65290111-65290130 chr14:65290112-65290121 chr14:65290209-65290223 chr14:65290274-65290283
10	CTCF	chr14:65289986-65290266	LNCaP	prostate:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
11	CTCF	chr14:65289832-65290366	MCF-7	breast:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
12	CTCF	chr14:65289876-65290314	A549	lung:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
13	CTCF	chr14:65289906-65290273	ECC-1	luminal epithelium:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
14	CTCF	chr14:65289906-65290347	IMR90	lung:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
15	CTCF	chr14:65289840-65290339	A549	lung:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
16	RAD21	chr14:65289854-65290400	A549	lung:	n/a	chr14:65290112-65290126 chr14:65290111-65290130 chr14:65290112-65290121 chr14:65290209-65290223 chr14:65290274-65290283
17	RAD21	chr14:65289744-65290474	MCF-7	breast:	n/a	chr14:65290112-65290126 chr14:65290395-65290408 chr14:65290111-65290130 chr14:65290112-65290121 chr14:65290209-65290223 chr14:65290274-65290283
18	IRF4	chr14:65289926-65290333	GM12878	blood:	n/a	n/a
19	CTCF	chr14:65289980-65290249	Pancreas_OC	pancreas:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
20	MYC	chr14:65289971-65290287	MCF-7	breast:	n/a	n/a
21	CTCF	chr14:65289978-65290298	Kidney_OC	kidney:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
22	CTCF	chr14:65289972-65290247	GM13977	blood:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
23	CTCF	chr14:65288936-65290698	SK-N-SH	brain:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65289007-65289025 chr14:65289593-65289600 chr14:65290112-65290133
24	CTCF	chr14:65289880-65290349	H1-hESC	embryonic stem cell:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
25	ZNF263	chr14:65289826-65290873	HEK293-T-REx	kidney:	n/a	chr14:65290174-65290195
26	TCF3	chr14:65289949-65290321	GM12878	blood:	n/a	n/a
27	RAD21	chr14:65289819-65290433	H1-hESC	embryonic stem cell:	n/a	chr14:65290112-65290126 chr14:65290395-65290408 chr14:65290111-65290130 chr14:65290112-65290121 chr14:65290209-65290223 chr14:65290274-65290283
28	CTCF	chr14:65289912-65290252	K562	blood:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
29	CTCF	chr14:65290120-65290270	HFF-Myc	foreskin:	n/a	n/a
30	CTCF	chr14:65289970-65290266	Lung_OC	lung:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
31	CTCF	chr14:65289962-65290265	A549	lung:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
32	RAD21	chr14:65289933-65290379	IMR90	lung:	n/a	chr14:65290112-65290126 chr14:65290111-65290130 chr14:65290112-65290121 chr14:65290209-65290223 chr14:65290274-65290283
33	HMGN3	chr14:65289968-65290325	K562	blood:	n/a	n/a
34	CTCF	chr14:65289958-65290279	GM12878	blood:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
35	USF1	chr14:65289927-65290325	A549	lung:	n/a	n/a
36	RAD21	chr14:65289813-65290493	A549	lung:	n/a	chr14:65290112-65290126 chr14:65290395-65290408 chr14:65290111-65290130 chr14:65290112-65290121 chr14:65290209-65290223 chr14:65290274-65290283
37	JUND	chr14:65289935-65290334	K562	blood:	n/a	chr14:65290160-65290169
38	USF2	chr14:65290079-65290273	H1-hESC	embryonic stem cell:	n/a	n/a
39	RAD21	chr14:65289842-65290291	HepG2	liver:	n/a	chr14:65290112-65290126 chr14:65290111-65290130 chr14:65290112-65290121 chr14:65290209-65290223 chr14:65290274-65290283
40	TEAD4	chr14:65289964-65290298	H1-hESC	embryonic stem cell:	n/a	n/a
41	RCOR1	chr14:65289942-65290282	K562	blood:	n/a	n/a
42	CTCF	chr14:65289962-65290266	H1-hESC	embryonic stem cell:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
43	CTCF	chr14:65289945-65290341	K562	blood:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
44	RAD21	chr14:65289955-65290257	GM12878	blood:	n/a	chr14:65290112-65290126 chr14:65290111-65290130 chr14:65290112-65290121 chr14:65290209-65290223
45	RAD21	chr14:65289867-65290378	H1-hESC	embryonic stem cell:	n/a	chr14:65290112-65290126 chr14:65290111-65290130 chr14:65290112-65290121 chr14:65290209-65290223 chr14:65290274-65290283
46	MAZ	chr14:65290094-65290284	HepG2	liver:	n/a	n/a
47	RFX5	chr14:65289953-65290280	Hela-S3	cervix:	n/a	n/a
48	RAD21	chr14:65289974-65290291	K562	blood:	n/a	chr14:65290112-65290126 chr14:65290111-65290130 chr14:65290112-65290121 chr14:65290209-65290223 chr14:65290274-65290283
49	CTCF	chr14:65289957-65290280	Gliobla	brain:	n/a	chr14:65290113-65290121 chr14:65290110-65290128 chr14:65290112-65290133
50	CREB1	chr14:65289921-65290390	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:65290012..65290932-chr14:65377431..65378083,2	MCF-7	breast:
2	chr14:65284109..65285780-chr14:65289982..65291896,2	K562	blood:
3	chr14:65268349..65269036-chr14:65289885..65290600,4	MCF-7	breast:
4	chr14:65269057..65270107-chr14:65289880..65290862,3	MCF-7	breast:

Variant related genes	Relation type
SPTB	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs114813	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12587537	0.83[CEU][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1273204	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1695751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016522	0.83[CEU][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2269292	0.83[CHD][hapmap]
rs229609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs229611	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229616	0.90[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229618	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229667	0.87[CEU][hapmap]
rs229670	0.83[MEX][hapmap]
rs229673	0.84[MEX][hapmap]
rs2649196	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs28495181	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4027216	0.92[CHB][hapmap]
rs423927	1.00[CHB][hapmap]
rs438035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs229619	VTI1B	cis	cerebellum	SCAN
rs229619	CHURC1	cis	parietal	SCAN
rs229619	CHURC1	cis	lymphoblastoid	seeQTL
rs229619	CHURC1	cis	cerebellum	SCAN
rs229619	RAB15	Cis_1M	lymphoblastoid	RTeQTL
rs229619	CHURC1	Cis_1M	lymphoblastoid	RTeQTL
rs229619	GPHB5	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65289200-65290600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr14:65289200-65290800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr14:65289200-65291600	Genic enhancers	K562	blood
4	chr14:65289400-65290400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
5	chr14:65289400-65290600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr14:65289400-65290800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr14:65289400-65291200	Enhancers	Right Ventricle	heart
8	chr14:65289600-65290400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
9	chr14:65289600-65290400	Enhancers	Gastric	stomach
10	chr14:65289600-65290600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr14:65289600-65293600	Enhancers	Fetal Heart	heart
12	chr14:65289800-65290400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:65289800-65290400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
14	chr14:65289800-65290400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr14:65289800-65290400	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr14:65289800-65290400	Enhancers	Colon Smooth Muscle	Colon
17	chr14:65289800-65290400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr14:65289800-65290400	Bivalent Enhancer	Fetal Intestine Small	intestine
19	chr14:65289800-65290400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
20	chr14:65289800-65290400	Bivalent Enhancer	Fetal Stomach	stomach
21	chr14:65289800-65290400	Enhancers	Ovary	ovary
22	chr14:65289800-65290400	Enhancers	Spleen	Spleen
23	chr14:65289800-65290400	Enhancers	HSMM	muscle
24	chr14:65289800-65290600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr14:65289800-65290600	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr14:65289800-65290600	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr14:65289800-65290600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
28	chr14:65289800-65290600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
29	chr14:65289800-65290600	Enhancers	Liver	Liver
30	chr14:65289800-65290600	Enhancers	HSMMtube	muscle
31	chr14:65289800-65290800	Enhancers	Brain Cingulate Gyrus	brain
32	chr14:65289800-65290800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr14:65289800-65295200	Enhancers	Left Ventricle	heart
34	chr14:65290000-65290400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr14:65290000-65290400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr14:65290000-65290400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
37	chr14:65290000-65290400	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr14:65290000-65290400	Enhancers	Esophagus	oesophagus
39	chr14:65290000-65290400	Enhancers	Lung	lung
40	chr14:65290000-65290400	Enhancers	Placenta Amnion	Placenta Amnion
41	chr14:65290000-65290400	Enhancers	Stomach Mucosa	stomach
42	chr14:65290000-65290400	Enhancers	A549	lung
43	chr14:65290000-65290400	Enhancers	HMEC	breast
44	chr14:65290000-65290600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr14:65290000-65295200	Enhancers	Psoas Muscle	Psoas
46	chr14:65290200-65290400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
47	chr14:65290200-65290400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
48	chr14:65290200-65290400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr14:65290200-65290400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr14:65290200-65290400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung

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