Variant report

Variant	rs4259
Chromosome Location	chr7:30543734-30543735
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	MAZ	chr7:30543684-30544834	Hela-S3	cervix:	n/a	chr7:30544110-30544119
2	POLR2A	chr7:30543199-30545052	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:30543622-30545568	GM12891	blood:	n/a	n/a
4	REST	chr7:30543602-30544981	A549	lung:	n/a	chr7:30544016-30544029
5	MYC	chr7:30543630-30545220	NB4	blood:	n/a	chr7:30544110-30544119 chr7:30545195-30545205
6	CHD1	chr7:30543704-30543955	H1-hESC	embryonic stem cell:	n/a	n/a
7	MXI1	chr7:30543645-30544906	GM12878	blood:	n/a	n/a
8	MAX	chr7:30543666-30545146	HepG2	liver:	n/a	chr7:30544110-30544119
9	TBP	chr7:30543466-30545051	K562	blood:	n/a	n/a
10	MAX	chr7:30543721-30545233	SK-N-SH	brain:	n/a	chr7:30544110-30544119 chr7:30545195-30545205
11	POLR2A	chr7:30543690-30545291	HL-60	blood:	n/a	n/a
12	TBL1XR1	chr7:30543440-30543951	K562	blood:	n/a	n/a
13	MXI1	chr7:30541821-30545796	SK-N-SH	brain:	n/a	n/a
14	MAX	chr7:30543665-30545053	K562	blood:	n/a	chr7:30544110-30544119
15	MAX	chr7:30543730-30545199	A549	lung:	n/a	chr7:30544110-30544119
16	CEBPB	chr7:30543556-30544938	Hela-S3	cervix:	n/a	chr7:30544492-30544500
17	MAX	chr7:30543639-30545107	HepG2	liver:	n/a	chr7:30544110-30544119
18	MXI1	chr7:30543713-30545164	IMR90	lung:	n/a	n/a
19	MAX	chr7:30543363-30545125	NB4	blood:	n/a	chr7:30544110-30544119
20	MAZ	chr7:30543695-30545213	IMR90	lung:	n/a	chr7:30544110-30544119 chr7:30545195-30545205
21	SMARCC1	chr7:30543112-30544982	Hela-S3	cervix:	n/a	n/a
22	SIN3A	chr7:30543590-30544919	H1-hESC	embryonic stem cell:	n/a	n/a
23	SIN3A	chr7:30543494-30544921	GM12878	blood:	n/a	n/a
24	POLR2A	chr7:30543487-30545356	HepG2	liver:	n/a	n/a
25	HCFC1	chr7:30543552-30543956	K562	blood:	n/a	n/a
26	MAX	chr7:30543714-30544898	H1-hESC	embryonic stem cell:	n/a	chr7:30544110-30544119
27	POLR2A	chr7:30543482-30545008	IMR90	lung:	n/a	n/a
28	MAFK	chr7:30543671-30544824	Hela-S3	cervix:	n/a	n/a
29	BRCA1	chr7:30543378-30544958	Hela-S3	cervix:	n/a	n/a
30	HCFC1	chr7:30543433-30545229	Hela-S3	cervix:	n/a	n/a
31	GABPA	chr7:30543688-30545163	MCF-7	breast:	n/a	n/a
32	SIN3AK20	chr7:30543561-30545133	PANC-1	pancreas:	n/a	n/a
33	E2F6	chr7:30543689-30545157	A549	lung:	n/a	chr7:30544532-30544541 chr7:30544447-30544458 chr7:30544492-30544501
34	SIN3AK20	chr7:30543626-30545340	MCF-7	breast:	n/a	n/a
35	POLR2A	chr7:30542394-30545283	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:30516309..30520214-chr7:30539829..30545899,10	MCF-7	breast:
2	chr7:30514482..30520047-chr7:30541597..30545999,6	K562	blood:
3	chr7:30543086..30546896-chr7:30587990..30592067,4	MCF-7	breast:
4	chr7:30542906..30546609-chr7:30564616..30567471,3	K562	blood:
5	chr7:30177889..30180137-chr7:30541048..30543861,2	K562	blood:
6	chr7:30540102..30542723-chr7:30542755..30545795,4	K562	blood:
7	chr7:30470137..30472560-chr7:30542746..30544397,2	MCF-7	breast:
8	chr7:30322508..30325162-chr7:30542047..30544631,2	K562	blood:
9	chr7:30537384..30539209-chr7:30541692..30544270,2	MCF-7	breast:
10	chr7:30537997..30542227-chr7:30542503..30545909,8	MCF-7	breast:
11	chr7:30516697..30519938-chr7:30542758..30546445,6	K562	blood:
12	chr7:30516038..30518897-chr7:30540788..30545615,6	MCF-7	breast:

Variant related genes	Relation type
GGCT	TF binding region
ENSG00000196295	Chromatin interaction
ENSG00000006625	Chromatin interaction
ENSG00000180233	Chromatin interaction
ENSG00000263683	Chromatin interaction
ENSG00000106100	Chromatin interaction
ENSG00000264520	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs28679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38406	0.85[ASN][1000 genomes]
rs38407	0.84[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs38408	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38409	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs38410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38413	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38414	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38415	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[ASN][1000 genomes]
rs38416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38417	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38418	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38419	0.97[ASN][1000 genomes]
rs38420	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38421	0.92[ASN][1000 genomes]
rs38422	0.97[ASN][1000 genomes]
rs38423	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38425	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38426	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38427	0.97[ASN][1000 genomes]
rs38428	0.87[ASN][1000 genomes]
rs38429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38430	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38432	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38433	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38434	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38435	0.85[ASN][1000 genomes]
rs38436	0.85[ASN][1000 genomes]
rs38437	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs38438	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38440	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs38441	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38442	0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38443	0.83[ASN][1000 genomes]
rs38444	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38445	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38446	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38447	0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38448	0.88[ASN][1000 genomes]
rs38450	0.81[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38451	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38452	0.88[ASN][1000 genomes]
rs38453	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38454	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38455	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38456	0.87[ASN][1000 genomes]
rs38458	0.87[ASN][1000 genomes]
rs38460	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38461	0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs38462	0.87[ASN][1000 genomes]
rs38463	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38464	0.87[ASN][1000 genomes]
rs38465	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38466	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs38467	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38468	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38469	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs38471	0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38472	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38473	0.80[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs38474	0.81[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs38478	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs38480	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs38481	0.81[ASN][1000 genomes]
rs38482	0.88[EUR][1000 genomes]
rs38483	0.80[ASN][1000 genomes]
rs39738	0.90[CHB][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs40237	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4258	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4259	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs4259	AC005154.8	cis	Whole Blood	GTEx
rs4259	AC005154.6	cis	Esophagus Muscularis	GTEx
rs4259	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs4259	AC005154.6	cis	Nerve Tibial	GTEx
rs4259	AC005154.6	cis	lung	GTEx
rs4259	AC005154.6	cis	Muscle Skeletal	GTEx
rs4259	AC005154.6	cis	Thyroid	GTEx
rs4259	AC005154.6	cis	Stomach	GTEx
rs4259	AC005154.6	cis	Esophagus Mucosa	GTEx
rs4259	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs4259	AC005154.6	cis	Whole Blood	GTEx
rs4259	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs4259	AC005154.6	cis	Artery Aorta	GTEx
rs4259	AC005154.6	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30542000-30543800	Flanking Active TSS	HMEC	breast
2	chr7:30542000-30543800	Flanking Active TSS	NHEK	skin
3	chr7:30542400-30545600	Active TSS	NHLF	lung
4	chr7:30542600-30544000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:30542800-30544200	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr7:30542800-30544200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr7:30542800-30544400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr7:30542800-30545200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:30543000-30543800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr7:30543000-30543800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr7:30543000-30543800	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr7:30543000-30543800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr7:30543000-30543800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr7:30543000-30543800	Flanking Active TSS	NH-A	brain
15	chr7:30543000-30544000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr7:30543000-30544000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr7:30543000-30544000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr7:30543000-30544000	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr7:30543000-30544000	Flanking Active TSS	Liver	Liver
20	chr7:30543000-30544000	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr7:30543000-30544000	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr7:30543000-30544000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr7:30543000-30544000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr7:30543000-30544000	Flanking Active TSS	HUVEC	blood vessel
25	chr7:30543000-30544000	Flanking Active TSS	Osteobl	bone
26	chr7:30543000-30544200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:30543000-30544800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:30543000-30545200	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr7:30543200-30543800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:30543200-30543800	Flanking Active TSS	Brain Angular Gyrus	brain
31	chr7:30543200-30543800	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr7:30543200-30543800	Flanking Active TSS	Fetal Lung	lung
33	chr7:30543200-30543800	Flanking Active TSS	Dnd41	blood
34	chr7:30543200-30543800	Flanking Active TSS	K562	blood
35	chr7:30543200-30544000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr7:30543200-30544000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr7:30543200-30544000	Flanking Active TSS	Brain Cingulate Gyrus	brain
38	chr7:30543200-30544000	Flanking Active TSS	Fetal Brain Male	brain
39	chr7:30543200-30544000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr7:30543200-30544000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr7:30543200-30544800	Active TSS	Fetal Intestine Small	intestine
42	chr7:30543200-30545000	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr7:30543200-30545200	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr7:30543200-30545200	Active TSS	HSMMtube	muscle
45	chr7:30543200-30545400	Active TSS	A549	lung
46	chr7:30543400-30543800	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr7:30543400-30543800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr7:30543400-30543800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr7:30543400-30543800	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr7:30543400-30543800	Active TSS	Colonic Mucosa	Colon

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