Variant report

Variant	rs6440001
Chromosome Location	chr3:141085972-141085973
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	POLR2A	chr3:141085700-141086380	K562	blood:	n/a	n/a
2	RCOR1	chr3:141085835-141086550	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:141085195-141089788	MCF10A-Er-Src	breast:	n/a	n/a
4	GATA1	chr3:141085140-141086022	PBDE	blood:	n/a	n/a
5	GATA3	chr3:141084947-141086783	SK-N-SH	brain:	n/a	n/a
6	MAX	chr3:141085146-141088115	HCT-116	colon:	n/a	n/a
7	POLR2A	chr3:141085894-141086320	A549	lung:	n/a	n/a
8	POLR2A	chr3:141085238-141086327	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:141085031-141086551	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr3:141085358-141086535	HepG2	liver:	n/a	n/a
11	MAX	chr3:141085836-141088223	HCT-116	colon:	n/a	n/a
12	POLR2A	chr3:141085898-141086514	GM12892	blood:	n/a	n/a
13	RAD21	chr3:141085156-141086578	IMR90	lung:	n/a	chr3:141086011-141086020 chr3:141086261-141086270
14	E2F6	chr3:141085718-141086560	A549	lung:	n/a	n/a
15	STAT3	chr3:141084899-141086673	MCF10A-Er-Src	breast:	n/a	chr3:141085616-141085624
16	MAZ	chr3:141085456-141086144	K562	blood:	n/a	n/a
17	JUND	chr3:141084716-141088288	SK-N-SH	brain:	n/a	chr3:141084974-141084986 chr3:141087277-141087288 chr3:141087860-141087872
18	MAX	chr3:141085203-141086657	SK-N-SH	brain:	n/a	n/a
19	FOSL2	chr3:141084905-141088629	A549	lung:	n/a	chr3:141088454-141088465 chr3:141088456-141088468 chr3:141084974-141084986 chr3:141088457-141088467 chr3:141087860-141087872
20	TCF7L2	chr3:141085094-141086480	Hela-S3	cervix:	n/a	n/a
21	NR3C1	chr3:141085926-141086435	A549	lung:	n/a	n/a
22	POLR2A	chr3:141085735-141086317	Gliobla	brain:	n/a	n/a
23	JUND	chr3:141085444-141085994	K562	blood:	n/a	n/a
24	MAX	chr3:141084953-141088456	A549	lung:	n/a	n/a
25	POLR2A	chr3:141085901-141086316	SK-N-SH	brain:	n/a	n/a
26	CEBPB	chr3:141084981-141086565	IMR90	lung:	n/a	n/a
27	POLR2A	chr3:141084808-141089686	U87	brain:	n/a	n/a
28	MAFK	chr3:141085243-141086603	IMR90	lung:	n/a	chr3:141086227-141086241
29	BCL3	chr3:141084578-141086541	A549	lung:	n/a	n/a
30	E2F6	chr3:141085900-141086473	A549	lung:	n/a	n/a
31	POLR2A	chr3:141085966-141087823	Hela-S3	cervix:	n/a	n/a
32	EP300	chr3:141085141-141086699	SK-N-SH	brain:	n/a	chr3:141085223-141085237
33	FOXP2	chr3:141085940-141086383	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr3:141085587-141086553	GM12892	blood:	n/a	n/a
35	SP1	chr3:141084804-141087897	A549	lung:	n/a	chr3:141087200-141087211 chr3:141085551-141085561 chr3:141087138-141087149
36	STAT3	chr3:141084861-141086839	MCF10A-Er-Src	breast:	n/a	chr3:141085616-141085624
37	FOSL2	chr3:141085026-141086684	SK-N-SH	brain:	n/a	n/a
38	EP300	chr3:141084883-141086677	SK-N-SH	brain:	n/a	chr3:141085223-141085237
39	JUN	chr3:141085260-141089964	K562	blood:	n/a	chr3:141089573-141089582 chr3:141088454-141088465 chr3:141088456-141088468 chr3:141089786-141089800 chr3:141088457-141088467 chr3:141087860-141087872
40	RCOR1	chr3:141085735-141086580	K562	blood:	n/a	n/a
41	FOS	chr3:141085113-141087652	MCF10A-Er-Src	breast:	n/a	chr3:141087277-141087288
42	RXRA	chr3:141085398-141086641	SK-N-SH	brain:	n/a	n/a
43	USF1	chr3:141085071-141086277	A549	lung:	n/a	n/a
44	EP300	chr3:141084742-141087945	A549	lung:	n/a	chr3:141087118-141087125 chr3:141087838-141087852 chr3:141087841-141087855 chr3:141087839-141087853 chr3:141087840-141087854 chr3:141085223-141085237
45	MYC	chr3:141085027-141086705	MCF10A-Er-Src	breast:	n/a	n/a
46	TCF12	chr3:141084582-141087938	SK-N-SH	brain:	n/a	chr3:141086726-141086734 chr3:141087130-141087140
47	GATA2	chr3:141085164-141088160	HUVEC	blood vessel:	n/a	chr3:141087801-141087808
48	REST	chr3:141084896-141086599	A549	lung:	n/a	chr3:141085326-141085344
49	TEAD4	chr3:141084952-141086627	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr3:141085904-141086595	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:141041261..141043649-chr3:141085742..141087985,3	K562	blood:
2	chr3:141041261..141045456-chr3:141085742..141089187,4	K562	blood:
3	chr3:141085384..141087888-chr3:141119776..141122327,3	MCF-7	breast:
4	chr3:141085187..141087816-chr3:141204878..141206678,4	MCF-7	breast:
5	chr3:141084115..141086523-chr3:141087109..141089663,3	MCF-7	breast:
6	chr3:141085737..141089975-chr3:141204779..141207356,5	K562	blood:
7	chr3:141084785..141090037-chr3:141119214..141123075,16	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TFDP2-2	chr3:141085886-141085979	ENSG00000249417.1

Variant related genes	Relation type
ZBTB38	TF binding region
ENSG00000177311	Chromatin interaction
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13098180	0.88[EUR][1000 genomes]
rs1346408	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16851367	0.80[ASN][1000 genomes]
rs1863868	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs2311847	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs4683603	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440006	0.81[CEU][hapmap]
rs6763931	0.81[CEU][hapmap]
rs6781636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6784404	0.96[CEU][hapmap];0.93[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7613516	0.81[ASW][hapmap];0.96[CEU][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs7624084	0.89[CEU][hapmap]
rs9838625	0.81[ASW][hapmap]
rs9866391	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141080200-141086800	Weak transcription	Fetal Thymus	thymus
2	chr3:141080600-141086200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:141080800-141086400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:141083600-141087400	Enhancers	NHDF-Ad	bronchial
5	chr3:141084000-141086800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:141084000-141086800	Enhancers	NHLF	lung
7	chr3:141084000-141087400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:141084200-141086600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:141084200-141086600	Enhancers	HepG2	liver
10	chr3:141084200-141086800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:141084200-141086800	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr3:141084200-141087400	Genic enhancers	Fetal Intestine Small	intestine
13	chr3:141084200-141087400	Enhancers	Placenta	Placenta
14	chr3:141084400-141087200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:141084600-141086600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:141084600-141086800	Enhancers	HUVEC	blood vessel
17	chr3:141084800-141086200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:141084800-141086200	Flanking Active TSS	NHEK	skin
19	chr3:141084800-141086600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:141084800-141086800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr3:141084800-141086800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr3:141084800-141086800	Enhancers	Adipose Nuclei	Adipose
23	chr3:141084800-141086800	Enhancers	Brain Substantia Nigra	brain
24	chr3:141084800-141086800	Enhancers	Colonic Mucosa	Colon
25	chr3:141084800-141086800	Enhancers	Fetal Lung	lung
26	chr3:141084800-141086800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr3:141084800-141087000	Enhancers	Fetal Heart	heart
28	chr3:141084800-141087800	Enhancers	Placenta Amnion	Placenta Amnion
29	chr3:141084800-141088400	Flanking Active TSS	A549	lung
30	chr3:141085000-141086200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:141085000-141086800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:141085000-141086800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:141085000-141086800	Enhancers	Brain Anterior Caudate	brain
34	chr3:141085000-141086800	Enhancers	Colon Smooth Muscle	Colon
35	chr3:141085000-141087000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:141085000-141087000	Enhancers	Fetal Stomach	stomach
37	chr3:141085200-141086000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:141085200-141086200	Flanking Active TSS	Osteobl	bone
39	chr3:141085200-141086800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:141085200-141086800	Enhancers	Stomach Mucosa	stomach
41	chr3:141085200-141087000	Enhancers	Pancreas	Pancrea
42	chr3:141085200-141087400	Enhancers	Fetal Kidney	kidney
43	chr3:141085200-141087400	Enhancers	Left Ventricle	heart
44	chr3:141085200-141087400	Enhancers	Right Atrium	heart
45	chr3:141085200-141087400	Enhancers	Right Ventricle	heart
46	chr3:141085200-141088000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:141085200-141088400	Enhancers	Small Intestine	intestine
48	chr3:141085400-141086000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr3:141085400-141086000	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr3:141085400-141086200	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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