Variant report

Variant	rs9378221
Chromosome Location	chr6:30181834-30181835
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	TCF7L2	chr6:30181766-30182204	PANC-1	pancreas:	n/a	n/a
2	E2F6	chr6:30181786-30182195	K562	blood:	n/a	chr6:30182075-30182085 chr6:30182017-30182027 chr6:30181933-30181942
3	SIN3AK20	chr6:30180528-30182503	MCF-7	breast:	n/a	n/a
4	POLR2A	chr6:30180595-30182425	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr6:30180548-30182444	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr6:30180643-30182514	Hela-S3	cervix:	n/a	n/a
7	CREB1	chr6:30181746-30182290	H1-hESC	embryonic stem cell:	n/a	n/a
8	GTF2F1	chr6:30180745-30182003	Hela-S3	cervix:	n/a	n/a
9	ATF2	chr6:30181567-30181968	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr6:30180618-30182493	HCT-116	colon:	n/a	n/a
11	CHD2	chr6:30180500-30182254	H1-hESC	embryonic stem cell:	n/a	n/a
12	TCF3	chr6:30181820-30182244	GM12878	blood:	n/a	n/a
13	TBP	chr6:30181109-30182057	Hela-S3	cervix:	n/a	n/a
14	YY1	chr6:30181262-30182253	SK-N-SH	brain:	n/a	chr6:30182080-30182089
15	RFX5	chr6:30180770-30182256	HepG2	liver:	n/a	n/a
16	EBF1	chr6:30181159-30182099	GM12878	blood:	n/a	n/a
17	ELF1	chr6:30180706-30182437	HCT-116	colon:	n/a	chr6:30182080-30182089 chr6:30182119-30182128
18	HEY1	chr6:30180902-30182414	HepG2	liver:	n/a	n/a
19	POLR2A	chr6:30181824-30182361	H1-hESC	embryonic stem cell:	n/a	n/a
20	PML	chr6:30181758-30182272	MCF-7	breast:	n/a	n/a
21	POLR2A	chr6:30180625-30182700	GM12892	blood:	n/a	n/a
22	TAF1	chr6:30181687-30182206	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:30180868-30182424	HepG2	liver:	n/a	n/a
24	WRNIP1	chr6:30181327-30181875	GM12878	blood:	n/a	n/a
25	GTF2F1	chr6:30180995-30182229	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr6:30180647-30182600	GM12878	blood:	n/a	n/a
27	MAX	chr6:30180540-30182416	ECC-1	luminal epithelium:	n/a	chr6:30181938-30181948
28	E2F6	chr6:30181073-30182266	K562	blood:	n/a	chr6:30181418-30181426 chr6:30181418-30181425 chr6:30181418-30181429 chr6:30182075-30182085 chr6:30181418-30181426 chr6:30181418-30181429 chr6:30181415-30181432 chr6:30182017-30182027 chr6:30181933-30181942 chr6:30181418-30181429 chr6:30181415-30181432
29	POLR2A	chr6:30180768-30182312	GM12891	blood:	n/a	n/a
30	EP300	chr6:30180982-30182450	ECC-1	luminal epithelium:	n/a	chr6:30180990-30181006 chr6:30181363-30181377 chr6:30182078-30182087 chr6:30182017-30182033
31	EGR1	chr6:30181833-30182048	GM12878	blood:	n/a	chr6:30181934-30181947
32	RELA	chr6:30180716-30182511	GM15510	blood:	n/a	n/a
33	ZNF143	chr6:30181797-30182179	GM12878	blood:	n/a	chr6:30181978-30181996
34	ZNF143	chr6:30180846-30182198	H1-hESC	embryonic stem cell:	n/a	chr6:30182170-30182180 chr6:30181978-30181996 chr6:30181336-30181346
35	EP300	chr6:30181003-30182089	GM12878	blood:	n/a	chr6:30181363-30181377 chr6:30182078-30182087 chr6:30182017-30182033
36	YY1	chr6:30180792-30182258	GM12892	blood:	n/a	chr6:30182080-30182089
37	POLR2A	chr6:30181817-30182160	K562	blood:	n/a	n/a
38	POLR2A	chr6:30181734-30182237	U87	brain:	n/a	n/a
39	POLR2A	chr6:30180707-30182590	HL-60	blood:	n/a	n/a
40	MAX	chr6:30180503-30182252	Hela-S3	cervix:	n/a	chr6:30181938-30181948
41	POLR2A	chr6:30180590-30182779	GM12878	blood:	n/a	n/a
42	MAX	chr6:30180696-30182482	HCT-116	colon:	n/a	chr6:30181938-30181948
43	ELF1	chr6:30181682-30182287	SK-N-SH	brain:	n/a	chr6:30182080-30182089 chr6:30182119-30182128
44	MAZ	chr6:30181754-30182387	Hela-S3	cervix:	n/a	chr6:30181938-30181948
45	POLR2A	chr6:30181721-30182280	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr6:30180653-30182387	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr6:30181785-30182342	HepG2	liver:	n/a	n/a
48	POLR2A	chr6:30181680-30182331	HUVEC	blood vessel:	n/a	n/a
49	MXI1	chr6:30180760-30182505	HepG2	liver:	n/a	n/a
50	PAX5	chr6:30181762-30182162	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30033185..30035212-chr6:30180473..30182741,2	MCF-7	breast:
2	chr6:30181151..30182089-chr9:130692947..130693639,2	Hela-S3	cervix:
3	chr6:30156337..30158600-chr6:30180750..30182606,2	MCF-7	breast:
4	chr6:30178310..30184484-chr6:30311860..30320436,13	MCF-7	breast:
5	chr6:30181004..30182231-chr7:27779467..27780336,3	Hela-S3	cervix:
6	chr15:75744964..75747465-chr6:30180922..30182722,2	MCF-7	breast:
7	chr17:27052665..27053186-chr6:30181676..30182430,2	Hela-S3	cervix:
8	chr6:30180733..30183619-chr6:30310467..30312981,3	MCF-7	breast:
9	chr6:30068684..30075353-chr6:30179679..30184952,7	MCF-7	breast:
10	chr6:30178635..30184988-chr6:30292357..30296104,9	MCF-7	breast:
11	chr6:30181485..30183400-chr6:30291563..30295527,5	MCF-7	breast:

Variant related genes	Relation type
TRIM26	TF binding region
ENSG00000204616	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000234127	Chromatin interaction
ENSG00000231226	Chromatin interaction
ENSG00000229893	Chromatin interaction
ENSG00000106052	Chromatin interaction
ENSG00000204619	Chromatin interaction
ENSG00000224372	Chromatin interaction
ENSG00000204599	Chromatin interaction
ENSG00000231074	Chromatin interaction
ENSG00000160602	Chromatin interaction
ENSG00000169375	Chromatin interaction
ENSG00000233892	Chromatin interaction
ENSG00000167103	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12175655	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12660499	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17188113	0.82[ASN][1000 genomes]
rs2074477	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2187980	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2239531	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2284167	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2284171	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517602	0.90[ASN][1000 genomes]
rs28730510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41272587	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41272591	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4282437	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56307380	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62407543	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9348838	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9366754	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9378189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380156	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9391677	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9391802	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9405046	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9378221	TRIM26	Cis_1M	lymphoblastoid	RTeQTL
rs9378221	HCG18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30179400-30182400	Active TSS	Fetal Intestine Small	intestine
2	chr6:30179600-30182200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:30179600-30182400	Active TSS	Esophagus	oesophagus
4	chr6:30179800-30182200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:30179800-30182200	Active TSS	Colonic Mucosa	Colon
6	chr6:30179800-30182400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:30179800-30182400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:30179800-30182400	Active TSS	Aorta	Aorta
9	chr6:30179800-30182400	Active TSS	A549	lung
10	chr6:30179800-30182600	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr6:30179800-30182600	Active TSS	Lung	lung
12	chr6:30180000-30182200	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr6:30180000-30182200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:30180000-30182200	Active TSS	Fetal Thymus	thymus
15	chr6:30180000-30182400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr6:30180000-30182400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr6:30180000-30182400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:30180000-30182400	Active TSS	Fetal Intestine Large	intestine
19	chr6:30180000-30182400	Active TSS	Right Ventricle	heart
20	chr6:30180000-30182600	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr6:30180000-30182600	Active TSS	H9 Cell Line	embryonic stem cell
22	chr6:30180000-30182600	Active TSS	Psoas Muscle	Psoas
23	chr6:30180000-30182600	Active TSS	Right Atrium	heart
24	chr6:30180200-30182000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:30180200-30182000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:30180200-30182200	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr6:30180200-30182200	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr6:30180200-30182200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:30180200-30182400	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr6:30180200-30182400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:30180200-30182400	Active TSS	Brain Substantia Nigra	brain
32	chr6:30180200-30182400	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr6:30180200-30182400	Active TSS	Stomach Mucosa	stomach
34	chr6:30180200-30182400	Active TSS	NHDF-Ad	bronchial
35	chr6:30180200-30182400	Active TSS	NHLF	lung
36	chr6:30180200-30182600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:30180200-30182600	Active TSS	Fetal Lung	lung
38	chr6:30180200-30182600	Active TSS	HSMMtube	muscle
39	chr6:30180200-30182800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:30180400-30182000	Active TSS	Fetal Brain Female	brain
41	chr6:30180400-30182200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:30180400-30182200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:30180400-30182200	Active TSS	Brain Anterior Caudate	brain
44	chr6:30180400-30182200	Active TSS	Fetal Heart	heart
45	chr6:30180400-30182200	Active TSS	Rectal Smooth Muscle	rectum
46	chr6:30180400-30182400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr6:30180400-30182400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:30180400-30182400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:30180400-30182400	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr6:30180400-30182400	Active TSS	Brain Cingulate Gyrus	brain

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