Variant report

Variant	rs28675035
Chromosome Location	chr7:66385996-66385997
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	MAX	chr7:66385713-66386358	A549	lung:	n/a	n/a
2	TEAD4	chr7:66385644-66386355	K562	blood:	n/a	n/a
3	GABPA	chr7:66385765-66386367	MCF-7	breast:	n/a	n/a
4	BCLAF1	chr7:66385669-66386385	GM12878	blood:	n/a	chr7:66386247-66386256 chr7:66386246-66386259
5	POLR2A	chr7:66385825-66387309	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr7:66385638-66386406	HL-60	blood:	n/a	n/a
7	MAX	chr7:66385653-66386407	ECC-1	luminal epithelium:	n/a	chr7:66386351-66386360
8	BCLAF1	chr7:66385693-66386379	GM12878	blood:	n/a	chr7:66386247-66386256 chr7:66386246-66386259
9	MAX	chr7:66385787-66386146	H1-hESC	embryonic stem cell:	n/a	n/a
10	CREB1	chr7:66385629-66386425	K562	blood:	n/a	n/a
11	MYC	chr7:66385670-66386502	A549	lung:	n/a	chr7:66386351-66386360
12	EP300	chr7:66385836-66386364	GM12878	blood:	n/a	chr7:66386196-66386210 chr7:66386195-66386209 chr7:66386052-66386065
13	POLR2A	chr7:66385727-66386417	Hela-S3	cervix:	n/a	n/a
14	IRF4	chr7:66385709-66386234	GM12878	blood:	n/a	n/a
15	REST	chr7:66385617-66386361	A549	lung:	n/a	chr7:66386304-66386317
16	STAT3	chr7:66385994-66386241	MCF10A-Er-Src	breast:	n/a	n/a
17	CEBPB	chr7:66385753-66386344	Hela-S3	cervix:	n/a	n/a
18	MAX	chr7:66385693-66386239	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr7:66385724-66386379	U87	brain:	n/a	n/a
20	PML	chr7:66385548-66387308	GM12878	blood:	n/a	n/a
21	MYC	chr7:66385797-66386326	HepG2	liver:	n/a	n/a
22	YY1	chr7:66385791-66386367	GM12891	blood:	n/a	chr7:66386247-66386261 chr7:66386246-66386255 chr7:66386246-66386260
23	TCF12	chr7:66385798-66386410	GM12878	blood:	n/a	chr7:66386401-66386408 chr7:66386400-66386410
24	GABPA	chr7:66385656-66386450	SK-N-SH	brain:	n/a	n/a
25	MYC	chr7:66385804-66386349	H1-hESC	embryonic stem cell:	n/a	n/a
26	STAT3	chr7:66385856-66386248	MCF10A-Er-Src	breast:	n/a	n/a
27	BHLHE40	chr7:66385672-66386407	K562	blood:	n/a	chr7:66386246-66386262 chr7:66386305-66386321
28	BATF	chr7:66385761-66386158	GM12878	blood:	n/a	n/a
29	CBX3	chr7:66385695-66386251	K562	blood:	n/a	n/a
30	TCF12	chr7:66385792-66386265	A549	lung:	n/a	n/a
31	POLR2A	chr7:66385676-66386433	PFSK-1	brain:	n/a	n/a
32	MAX	chr7:66385587-66386429	SK-N-SH	brain:	n/a	chr7:66386351-66386360
33	SIN3AK20	chr7:66385917-66386284	PANC-1	pancreas:	n/a	n/a
34	ELF1	chr7:66385724-66386381	SK-N-SH	brain:	n/a	chr7:66386085-66386098 chr7:66386246-66386255 chr7:66386089-66386098 chr7:66386088-66386097 chr7:66386247-66386259
35	POLR2A	chr7:66385857-66386345	H1-hESC	embryonic stem cell:	n/a	n/a
36	RELA	chr7:66385771-66386277	GM18951	blood:	n/a	n/a
37	CREB1	chr7:66385673-66386503	A549	lung:	n/a	n/a
38	ELF1	chr7:66385666-66386464	K562	blood:	n/a	chr7:66386085-66386098 chr7:66386246-66386255 chr7:66386412-66386424 chr7:66386089-66386098 chr7:66386088-66386097 chr7:66386247-66386259
39	HDAC2	chr7:66385750-66386414	HepG2	liver:	n/a	chr7:66386200-66386214 chr7:66386199-66386213 chr7:66386197-66386211 chr7:66386198-66386212 chr7:66386196-66386210 chr7:66386195-66386209
40	HEY1	chr7:66385654-66386443	HepG2	liver:	n/a	chr7:66386386-66386401 chr7:66386347-66386362
41	POLR2A	chr7:66385704-66386643	GM18951	blood:	n/a	n/a
42	ELF1	chr7:66385590-66386588	MCF-7	breast:	n/a	chr7:66386085-66386098 chr7:66386246-66386255 chr7:66386412-66386424 chr7:66386089-66386098 chr7:66386088-66386097 chr7:66386247-66386259
43	MYC	chr7:66385701-66386242	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr7:66385738-66386470	HCT-116	colon:	n/a	n/a
45	POLR2A	chr7:66385708-66386426	GM12891	blood:	n/a	n/a
46	POLR2A	chr7:66385303-66386473	Raji	blood:	n/a	n/a
47	SIN3AK20	chr7:66385933-66386357	PFSK-1	brain:	n/a	n/a
48	REST	chr7:66385691-66386260	SK-N-SH	brain:	n/a	n/a
49	YY1	chr7:66385752-66386555	K562	blood:	n/a	chr7:66386247-66386261 chr7:66386246-66386255 chr7:66386246-66386260
50	USF1	chr7:66385740-66386288	SK-N-SH_RA	brain:	n/a	chr7:66386246-66386262

No.	Distal block	Cell Line	Cell type
1	chr7:66385651..66388919-chr7:66460114..66462403,3	MCF-7	breast:
2	chr7:66385883..66386781-chr7:66459948..66460665,2	Hela-S3	cervix:
3	chr7:66092683..66094985-chr7:66385486..66387762,2	K562	blood:
4	chr7:66204784..66206359-chr7:66385620..66388278,2	MCF-7	breast:
5	chr7:66309154..66310879-chr7:66385975..66387792,2	MCF-7	breast:
6	chr7:66308191..66311276-chr7:66384066..66387492,7	MCF-7	breast:
7	chr7:66385169..66388074-chr7:66392898..66397062,6	MCF-7	breast:
8	chr7:66384595..66388317-chr7:66459135..66463010,5	K562	blood:
9	chr7:66308297..66310076-chr7:66385373..66388075,2	K562	blood:
10	chr7:66378566..66381625-chr7:66385153..66387745,3	MCF-7	breast:
11	chr7:66379191..66382749-chr7:66384574..66388642,5	K562	blood:
12	chr7:66385188..66388317-chr7:66459133..66463010,3	K562	blood:
13	chr12:110939415..110940003-chr7:66385750..66386337,2	NB4	blood:
14	chr7:66312126..66314998-chr7:66385416..66387725,2	MCF-7	breast:
15	chr7:66309510..66310213-chr7:66385838..66386579,2	MCF-7	breast:
16	chr7:66384799..66388848-chr7:66389441..66396879,12	K562	blood:
17	chr7:66385080..66386736-chr7:66393610..66396808,3	MCF-7	breast:
18	chr1:228353195..228353730-chr7:66385183..66386076,2	NB4	blood:

Variant related genes	Relation type
TMEM248	TF binding region
ENSG00000111237	Chromatin interaction
ENSG00000232546	Chromatin interaction
ENSG00000198874	Chromatin interaction
ENSG00000151164	Chromatin interaction
ENSG00000154710	Chromatin interaction
ENSG00000272831	Chromatin interaction
ENSG00000230583	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000106609	Chromatin interaction
ENSG00000243335	Chromatin interaction
ENSG00000126524	Chromatin interaction
ENSG00000179131	Chromatin interaction
ENSG00000181873	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10156059	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10224189	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10224536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs10226191	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10228964	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10231411	1.00[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs10234322	0.88[EUR][1000 genomes]
rs10234640	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10235638	0.82[EUR][1000 genomes]
rs10240582	0.85[EUR][1000 genomes]
rs10241395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10241528	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10242870	0.86[EUR][1000 genomes]
rs10244459	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10245017	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10247324	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10247815	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10256117	0.84[EUR][1000 genomes]
rs10263993	0.81[EUR][1000 genomes]
rs10264433	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10264555	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10265069	0.88[EUR][1000 genomes]
rs10266792	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10267253	0.86[EUR][1000 genomes]
rs10270326	0.84[EUR][1000 genomes]
rs10280816	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10281090	0.90[EUR][1000 genomes]
rs10282522	1.00[CEU][hapmap]
rs1060527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1064795	1.00[CEU][hapmap];0.91[TSI][hapmap]
rs13437994	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17680708	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17747927	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17748115	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17748222	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2013707	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28375318	0.83[EUR][1000 genomes]
rs28379824	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28472679	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28501161	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28533332	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28547918	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28607736	0.82[EUR][1000 genomes]
rs28634091	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28641990	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663128	0.85[EUR][1000 genomes]
rs28817095	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3778908	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3800814	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3800818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57774708	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57875851	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59693594	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60026498	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67408913	0.86[EUR][1000 genomes]
rs6964080	0.84[EUR][1000 genomes]
rs6965680	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6971508	0.91[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs6973897	0.85[EUR][1000 genomes]
rs71526586	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73135950	0.86[EUR][1000 genomes]
rs73135960	0.85[EUR][1000 genomes]
rs73135973	0.83[EUR][1000 genomes]
rs73137960	0.84[EUR][1000 genomes]
rs73137963	0.83[EUR][1000 genomes]
rs73139976	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73141980	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73143921	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73143998	0.88[EUR][1000 genomes]
rs73145911	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73145924	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73151646	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73151663	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73151665	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7455757	0.86[EUR][1000 genomes]
rs7777631	1.00[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs7785883	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796977	0.85[EUR][1000 genomes]
rs7809359	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809535	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs868960	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3324611	chr7:66383817-66388015	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28675035	GS1-124K5.12	cis	Adipose Subcutaneous	GTEx
rs28675035	CRCP	cis	parietal	SCAN
rs28675035	GUSB	cis	cerebellum	SCAN
rs28675035	VKORC1L1	cis	lymphoblastoid	seeQTL
rs28675035	GS1-124K5.12	cis	Skin Sun Exposed Lower leg	GTEx
rs28675035	GS1-124K5.12	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66384800-66387400	Active TSS	NHDF-Ad	bronchial
2	chr7:66385000-66387000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr7:66385000-66387200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr7:66385000-66388000	Active TSS	A549	lung
5	chr7:66385200-66386000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr7:66385200-66386800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:66385200-66387000	Active TSS	H1 Cell Line	embryonic stem cell
8	chr7:66385200-66387000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:66385200-66387000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:66385200-66387000	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr7:66385200-66387000	Active TSS	Fetal Brain Female	brain
12	chr7:66385200-66387000	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr7:66385200-66387000	Active TSS	Stomach Smooth Muscle	stomach
14	chr7:66385200-66387200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:66385200-66387200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr7:66385200-66387200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:66385200-66387200	Active TSS	Fetal Kidney	kidney
18	chr7:66385200-66387200	Active TSS	HMEC	breast
19	chr7:66385200-66387800	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr7:66385400-66386000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:66385400-66386000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:66385400-66386000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr7:66385400-66386000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:66385400-66386000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr7:66385400-66386000	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr7:66385400-66386000	Flanking Active TSS	Osteobl	bone
27	chr7:66385400-66386200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr7:66385400-66386200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr7:66385400-66386400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:66385400-66386800	Active TSS	Fetal Brain Male	brain
31	chr7:66385400-66387000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr7:66385400-66387000	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr7:66385400-66387000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr7:66385400-66387000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr7:66385400-66387000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr7:66385400-66387000	Active TSS	Brain Angular Gyrus	brain
37	chr7:66385400-66387000	Active TSS	Colon Smooth Muscle	Colon
38	chr7:66385400-66387000	Active TSS	Fetal Muscle Leg	muscle
39	chr7:66385400-66387200	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr7:66385400-66387200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr7:66385400-66387200	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr7:66385400-66387200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:66385400-66387400	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr7:66385400-66387400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr7:66385400-66387400	Active TSS	Psoas Muscle	Psoas
46	chr7:66385400-66387400	Active TSS	HSMMtube	muscle
47	chr7:66385400-66387600	Active TSS	Fetal Muscle Trunk	muscle
48	chr7:66385400-66387600	Active TSS	Thymus	Thymus
49	chr7:66385400-66388000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:66385400-66388200	Active TSS	Breast Myoepithelial Primary Cells	Breast

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