Variant report

Variant	rs3748079
Chromosome Location	chr6:33588147-33588148
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	POLR2A	chr6:33587814-33588686	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr6:33587972-33589359	PANC-1	pancreas:	n/a	n/a
3	NFIC	chr6:33588009-33589147	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr6:33587950-33590165	Hela-S3	cervix:	n/a	n/a
5	RCOR1	chr6:33588024-33588227	K562	blood:	n/a	n/a
6	MAX	chr6:33588051-33590088	ECC-1	luminal epithelium:	n/a	chr6:33589328-33589337 chr6:33589347-33589356 chr6:33589001-33589011
7	ELF1	chr6:33587855-33588234	A549	lung:	n/a	chr6:33588078-33588091 chr6:33588015-33588028
8	POLR2A	chr6:33587813-33588270	HCT-116	colon:	n/a	n/a
9	ELF1	chr6:33587879-33588455	GM12878	blood:	n/a	chr6:33588078-33588091 chr6:33588015-33588028
10	TFAP2A	chr6:33587780-33589508	Hela-S3	cervix:	n/a	chr6:33587936-33587950 chr6:33587938-33587948 chr6:33587936-33587950 chr6:33587938-33587948 chr6:33588821-33588836 chr6:33587938-33587948 chr6:33588733-33588744 chr6:33587938-33587948
11	POLR2A	chr6:33587666-33589182	U87	brain:	n/a	n/a
12	RUNX3	chr6:33587881-33588331	GM12878	blood:	n/a	n/a
13	TCF12	chr6:33587908-33588692	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr6:33587996-33590038	MCF10A-Er-Src	breast:	n/a	n/a
15	CTCF	chr6:33588140-33588290	HEEpiC	esophagus:	n/a	n/a
16	TEAD4	chr6:33587973-33588789	ECC-1	luminal epithelium:	n/a	n/a
17	ELF1	chr6:33587897-33588341	K562	blood:	n/a	chr6:33588078-33588091 chr6:33588015-33588028
18	CTCF	chr6:33588120-33588270	HBMEC	blood vessel:	n/a	n/a
19	SMARCC1	chr6:33586961-33588673	Hela-S3	cervix:	n/a	n/a
20	MAX	chr6:33587836-33590117	Hela-S3	cervix:	n/a	chr6:33589328-33589337 chr6:33589347-33589356 chr6:33589001-33589011
21	MAX	chr6:33587927-33589931	A549	lung:	n/a	chr6:33589328-33589337 chr6:33589347-33589356 chr6:33589001-33589011
22	SIN3A	chr6:33587857-33590046	H1-hESC	embryonic stem cell:	n/a	chr6:33587958-33587971 chr6:33589849-33589857 chr6:33588670-33588681 chr6:33587966-33587974
23	POLR2A	chr6:33587672-33589176	U87	brain:	n/a	n/a
24	CTCF	chr6:33588080-33588230	HRE	kidney:	n/a	n/a
25	SIN3AK20	chr6:33588003-33588354	PANC-1	pancreas:	n/a	n/a
26	CTCF	chr6:33588140-33588290	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr6:33587843-33588364	PANC-1	pancreas:	n/a	n/a
28	EBF1	chr6:33588062-33588415	GM12878	blood:	n/a	chr6:33588290-33588301
29	ZBTB7A	chr6:33587900-33588351	K562	blood:	n/a	n/a
30	MAX	chr6:33587775-33590168	HCT-116	colon:	n/a	chr6:33589328-33589337 chr6:33589347-33589356 chr6:33589001-33589011
31	ELF1	chr6:33587905-33588297	GM12878	blood:	n/a	chr6:33588078-33588091 chr6:33588015-33588028
32	CTCF	chr6:33588120-33588270	Hela-S3	cervix:	n/a	n/a
33	ZBTB7A	chr6:33587872-33588689	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr6:33587836-33589724	GM18505	blood:	n/a	n/a
35	MAZ	chr6:33587852-33590071	Hela-S3	cervix:	n/a	chr6:33589328-33589337 chr6:33589347-33589356
36	POLR2A	chr6:33588038-33588295	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr6:33587939-33589850	GM15510	blood:	n/a	n/a
38	ELK1	chr6:33588037-33588488	Hela-S3	cervix:	n/a	n/a
39	RCOR1	chr6:33587762-33588413	K562	blood:	n/a	n/a
40	POLR2A	chr6:33587236-33590289	HUVEC	blood vessel:	n/a	n/a
41	CTCF	chr6:33588040-33588190	GM06990	blood:	n/a	n/a
42	TFAP2C	chr6:33587771-33589488	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr6:33587828-33590873	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr6:33587743-33589942	SK-N-MC	brain:	n/a	n/a
45	POLR2A	chr6:33587978-33590022	GM12892	blood:	n/a	n/a
46	MAX	chr6:33587892-33590023	K562	blood:	n/a	chr6:33589328-33589337 chr6:33589347-33589356 chr6:33589001-33589011
47	MXI1	chr6:33587781-33590201	Hela-S3	cervix:	n/a	chr6:33589775-33589784
48	CTCF	chr6:33588120-33588270	HepG2	liver:	n/a	n/a
49	ELF1	chr6:33587791-33588324	K562	blood:	n/a	chr6:33588078-33588091 chr6:33588015-33588028
50	IRF1	chr6:33588036-33588949	K562	blood:	n/a	chr6:33588496-33588507 chr6:33588084-33588093 chr6:33588205-33588216 chr6:33588204-33588218 chr6:33588495-33588509

No.	Distal block	Cell Line	Cell type
1	chr6:33587976..33588692-chr7:152372698..152373478,2	Hela-S3	cervix:
2	chr18:18691523..18692461-chr6:33588062..33589054,2	Hela-S3	cervix:
3	chr17:56735246..56737826-chr6:33586590..33589099,2	MCF-7	breast:
4	chr6:33587172..33590152-chr6:34203876..34205466,2	K562	blood:
5	chr6:33550022..33555745-chr6:33586647..33590467,5	MCF-7	breast:
6	chr6:33551460..33554975-chr6:33588078..33592105,4	K562	blood:
7	chr6:33382580..33384156-chr6:33587956..33590051,2	K562	blood:
8	chr6:33587667..33592228-chr6:33677016..33679936,5	MCF-7	breast:

Variant related genes	Relation type
ITPR3	TF binding region
ENSG00000204188	Chromatin interaction
ENSG00000137288	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000196584	Chromatin interaction
ENSG00000067900	Chromatin interaction
ENSG00000137309	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12190817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205634	1.00[ASW][hapmap];0.86[AFR][1000 genomes]
rs12206050	0.86[MEX][hapmap];0.85[MKK][hapmap]
rs5745568	0.86[GIH][hapmap]
rs5745582	0.84[GIH][hapmap]
rs62407633	0.86[AFR][1000 genomes]
rs62407648	0.86[AFR][1000 genomes]
rs72882008	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9296095	0.84[GIH][hapmap];0.80[MEX][hapmap]
rs9461893	0.96[EUR][1000 genomes]
rs9469525	0.84[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9469527	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
5	nsv5250	chr6:33565017-33598370	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
6	esv1817557	chr6:33584788-33614127	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	esv1813933	chr6:33587443-33614127	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv3321796	chr6:33587999-33590547	Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3748079	CDKN1A	cis	parietal	SCAN
rs3748079	PIM1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33586600-33588200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:33586800-33588600	Flanking Bivalent TSS/Enh	HepG2	liver
3	chr6:33587000-33588200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
4	chr6:33587000-33588600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
5	chr6:33587200-33588600	Flanking Active TSS	HUVEC	blood vessel
6	chr6:33587200-33589000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:33587600-33588200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:33587600-33588200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
9	chr6:33587600-33588200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr6:33587600-33588200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr6:33587600-33588200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:33587600-33588200	Flanking Active TSS	HMEC	breast
13	chr6:33587600-33588200	Flanking Active TSS	HSMM	muscle
14	chr6:33587600-33588200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
15	chr6:33587600-33588600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr6:33587600-33588600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:33587600-33588600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
18	chr6:33587600-33589000	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr6:33587600-33589000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
20	chr6:33587600-33590000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:33587600-33590000	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr6:33587600-33590200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:33587800-33588200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:33587800-33588200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:33587800-33588200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr6:33587800-33588200	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr6:33587800-33588200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr6:33587800-33588200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr6:33587800-33588200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr6:33587800-33588200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:33587800-33588200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:33587800-33588200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:33587800-33588200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr6:33587800-33588200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr6:33587800-33588200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr6:33587800-33588200	Flanking Active TSS	Colonic Mucosa	Colon
37	chr6:33587800-33588200	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr6:33587800-33588200	Flanking Active TSS	Fetal Intestine Small	intestine
39	chr6:33587800-33588200	Flanking Active TSS	Placenta	Placenta
40	chr6:33587800-33588200	Flanking Active TSS	Right Ventricle	heart
41	chr6:33587800-33588200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr6:33587800-33588200	Flanking Active TSS	Thymus	Thymus
43	chr6:33587800-33588200	Flanking Active TSS	GM12878-XiMat	blood
44	chr6:33587800-33588200	Flanking Active TSS	K562	blood
45	chr6:33587800-33588200	Flanking Active TSS	NHEK	skin
46	chr6:33587800-33588200	Flanking Active TSS	Osteobl	bone
47	chr6:33587800-33588400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:33587800-33588400	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr6:33587800-33588400	Flanking Active TSS	Fetal Muscle Trunk	muscle
50	chr6:33587800-33588400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle

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