Variant report

Variant	rs2272924
Chromosome Location	chr6:143772311-143772312
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	GABPA	chr6:143771401-143772413	MCF-7	breast:	n/a	n/a
2	POLR2A	chr6:143771489-143772455	U87	brain:	n/a	n/a
3	POLR2A	chr6:143770519-143772427	K562	blood:	n/a	n/a
4	MAX	chr6:143770793-143772422	MCF-7	breast:	n/a	chr6:143771091-143771100 chr6:143771424-143771435 chr6:143772039-143772047 chr6:143771091-143771101 chr6:143771090-143771101 chr6:143771091-143771100 chr6:143771092-143771099 chr6:143771090-143771101 chr6:143771425-143771434
5	MAZ	chr6:143771166-143772486	IMR90	lung:	n/a	chr6:143771424-143771435 chr6:143772039-143772047 chr6:143771425-143771434
6	CREB1	chr6:143771560-143772387	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:143771068-143772311	K562	blood:	n/a	n/a
8	POLR2A	chr6:143771519-143772328	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr6:143771425-143772366	GM12891	blood:	n/a	n/a
10	MBD4	chr6:143770716-143772336	HepG2	liver:	n/a	n/a
11	NFYA	chr6:143771739-143772439	K562	blood:	n/a	n/a
12	CREB1	chr6:143771437-143772401	K562	blood:	n/a	n/a
13	POLR2A	chr6:143771219-143772408	ProgFib	skin:	n/a	n/a
14	POLR2A	chr6:143770844-143772478	GM18505	blood:	n/a	n/a
15	ARID3A	chr6:143771555-143772364	HepG2	liver:	n/a	n/a
16	BHLHE40	chr6:143770761-143772580	GM12878	blood:	n/a	chr6:143771425-143771434 chr6:143771425-143771434 chr6:143771943-143771959 chr6:143771960-143771976 chr6:143771957-143771973
17	SIN3AK20	chr6:143771467-143772427	HCT-116	colon:	n/a	n/a
18	POLR2A	chr6:143771429-143772443	GM12891	blood:	n/a	n/a
19	POLR2A	chr6:143770844-143772466	Raji	blood:	n/a	n/a
20	MXI1	chr6:143770998-143772405	K562	blood:	n/a	chr6:143771092-143771101
21	ZNF143	chr6:143771413-143772359	K562	blood:	n/a	chr6:143772347-143772356
22	RCOR1	chr6:143771354-143772421	HepG2	liver:	n/a	n/a
23	POLR2A	chr6:143771422-143772380	MCF-7	breast:	n/a	n/a
24	ZNF263	chr6:143771268-143772564	HEK293-T-REx	kidney:	n/a	n/a
25	POLR2A	chr6:143771144-143772405	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr6:143771457-143772332	GM12892	blood:	n/a	n/a
27	POLR2A	chr6:143770495-143772396	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr6:143770828-143772337	K562	blood:	n/a	n/a
29	POLR2A	chr6:143771025-143772388	HUVEC	blood vessel:	n/a	n/a
30	MYBL2	chr6:143770652-143772663	HepG2	liver:	n/a	n/a
31	ZNF384	chr6:143771678-143772341	K562	blood:	n/a	n/a
32	MAX	chr6:143770846-143772455	ECC-1	luminal epithelium:	n/a	chr6:143771091-143771100 chr6:143771424-143771435 chr6:143772039-143772047 chr6:143771091-143771101 chr6:143771090-143771101 chr6:143771091-143771100 chr6:143771092-143771099 chr6:143771090-143771101 chr6:143771425-143771434
33	POLR2A	chr6:143770685-143772368	K562	blood:	n/a	n/a
34	POLR2A	chr6:143771141-143772459	Hela-S3	cervix:	n/a	n/a
35	MYC	chr6:143770575-143772435	K562	blood:	n/a	chr6:143771091-143771100 chr6:143771424-143771435 chr6:143772039-143772047 chr6:143771091-143771101 chr6:143771090-143771101 chr6:143771091-143771100 chr6:143771092-143771099 chr6:143771090-143771101 chr6:143771425-143771434
36	ELK4	chr6:143771720-143772408	Hela-S3	cervix:	n/a	chr6:143771870-143771881
37	RCOR1	chr6:143770913-143772544	K562	blood:	n/a	n/a
38	BHLHE40	chr6:143770851-143772459	HepG2	liver:	n/a	chr6:143771425-143771434 chr6:143771425-143771434 chr6:143771943-143771959 chr6:143771960-143771976 chr6:143771957-143771973
39	GTF2F1	chr6:143770898-143772579	Hela-S3	cervix:	n/a	n/a
40	ATF3	chr6:143771653-143772346	K562	blood:	n/a	n/a
41	ELF1	chr6:143771495-143772328	GM12878	blood:	n/a	chr6:143771963-143771972
42	JUND	chr6:143770864-143772511	K562	blood:	n/a	n/a
43	POLR2A	chr6:143770832-143772317	HL-60	blood:	n/a	n/a
44	POLR2A	chr6:143770767-143772467	GM12892	blood:	n/a	n/a
45	NFIC	chr6:143770829-143772340	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:143771495-143772386	U87	brain:	n/a	n/a
47	POLR2A	chr6:143771233-143772553	HepG2	liver:	n/a	n/a
48	SIN3AK20	chr6:143771407-143772424	MCF-7	breast:	n/a	n/a
49	POLR2A	chr6:143770891-143772449	GM12878	blood:	n/a	n/a
50	WRNIP1	chr6:143770871-143772504	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:143770561..143773410-chr6:143856875..143861047,4	MCF-7	breast:
2	chr6:143769666..143773987-chr6:143831101..143834872,5	MCF-7	breast:
3	chr6:143758626..143760810-chr6:143770211..143772331,4	MCF-7	breast:
4	chr6:143770816..143772927-chr6:143831000..143833550,2	MCF-7	breast:
5	chr6:143771955..143774929-chr6:143804997..143806863,2	K562	blood:
6	chr6:143770206..143776731-chr6:143830754..143834661,9	K562	blood:
7	chr17:75277432..75280215-chr6:143771132..143773391,2	MCF-7	breast:
8	chr6:143770206..143773921-chr6:143828795..143834716,12	K562	blood:

Variant related genes	Relation type
ADAT2	TF binding region
ENSG00000001036	Chromatin interaction
ENSG00000268402	Chromatin interaction
ENSG00000229036	Chromatin interaction
ENSG00000034693	Chromatin interaction
ENSG00000263718	Chromatin interaction
ENSG00000184640	Chromatin interaction
ENSG00000112419	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1061220	0.92[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs1065355	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes]
rs10782288	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10782289	0.83[EUR][1000 genomes]
rs10809	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs1111355	0.84[ASN][1000 genomes]
rs12196227	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs12199192	0.82[EUR][1000 genomes]
rs1338533	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1424922	0.90[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1978529	0.84[EUR][1000 genomes]
rs2143137	0.82[CEU][hapmap];0.87[JPT][hapmap]
rs2294505	0.90[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs2294506	0.89[CEU][hapmap];0.88[JPT][hapmap]
rs2496590	0.88[ASN][1000 genomes]
rs2496593	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3088203	0.92[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs3761999	0.84[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs3762000	0.81[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3762001	0.83[CEU][hapmap];0.87[JPT][hapmap]
rs3762002	0.83[CEU][hapmap];0.87[JPT][hapmap]
rs3789790	0.83[CEU][hapmap];0.87[JPT][hapmap]
rs3804538	0.89[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs3804539	0.89[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes]
rs3804544	0.94[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes]
rs4895612	0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4895614	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4895615	0.89[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4896656	0.92[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4896659	0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4896660	0.90[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6924268	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6926733	0.90[CEU][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6929191	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6930325	0.90[CEU][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6935346	0.89[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6935618	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741976	0.89[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs7746655	0.83[ASN][1000 genomes]
rs9321913	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs9321914	0.89[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9373391	0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs9373393	0.89[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9376750	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs9376753	0.83[CEU][hapmap];0.87[JPT][hapmap]
rs9390090	0.89[ASN][1000 genomes]
rs9390092	0.92[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9390094	0.90[CEU][hapmap];0.84[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs9390096	0.83[CEU][hapmap]
rs9399442	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9399443	0.83[EUR][1000 genomes]
rs9403492	0.91[EUR][1000 genomes]
rs9403494	0.89[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs9403496	0.89[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2272924	PEX3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143769600-143772600	Active TSS	K562	blood
2	chr6:143770200-143772600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:143770400-143772600	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr6:143770400-143772600	Active TSS	A549	lung
5	chr6:143770400-143772800	Active TSS	Psoas Muscle	Psoas
6	chr6:143770600-143772400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr6:143770600-143772600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:143770600-143772600	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr6:143770600-143772600	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr6:143770600-143772600	Active TSS	HSMM	muscle
11	chr6:143770600-143772600	Active TSS	NHEK	skin
12	chr6:143770600-143772800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:143770600-143772800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr6:143770600-143772800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:143770600-143772800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:143770600-143773000	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr6:143770600-143773000	Active TSS	H1 Cell Line	embryonic stem cell
18	chr6:143770600-143773000	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr6:143770600-143773000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:143770600-143773000	Active TSS	Colonic Mucosa	Colon
21	chr6:143770600-143773000	Active TSS	Right Atrium	heart
22	chr6:143770600-143773000	Active TSS	Right Ventricle	heart
23	chr6:143770600-143773800	Active TSS	HMEC	breast
24	chr6:143770800-143772400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:143770800-143772400	Active TSS	Fetal Brain Male	brain
26	chr6:143770800-143772600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:143770800-143772600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:143770800-143772600	Active TSS	Esophagus	oesophagus
29	chr6:143770800-143772600	Active TSS	Gastric	stomach
30	chr6:143770800-143772600	Active TSS	Hela-S3	cervix
31	chr6:143770800-143772600	Active TSS	HSMMtube	muscle
32	chr6:143770800-143772800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr6:143770800-143772800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr6:143770800-143772800	Active TSS	Aorta	Aorta
35	chr6:143770800-143772800	Active TSS	Fetal Muscle Trunk	muscle
36	chr6:143770800-143773000	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr6:143770800-143773000	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr6:143770800-143773000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:143770800-143773200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:143770800-143773200	Active TSS	GM12878-XiMat	blood
41	chr6:143770800-143773200	Active TSS	NHDF-Ad	bronchial
42	chr6:143771000-143772400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:143771000-143772400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:143771000-143772400	Active TSS	Fetal Heart	heart
45	chr6:143771000-143772400	Active TSS	Small Intestine	intestine
46	chr6:143771000-143772400	Active TSS	Dnd41	blood
47	chr6:143771000-143772400	Bivalent/Poised TSS	HepG2	liver
48	chr6:143771000-143772600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:143771000-143772600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:143771000-143772600	Active TSS	Primary T helper naive cells from peripheral blood	blood

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