Variant report

Variant	rs6763927
Chromosome Location	chr3:141140366-141140367
allele	A/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	FOSL2	chr3:141140366-141140831	A549	lung:	n/a	chr3:141140587-141140598 chr3:141140591-141140599 chr3:141140589-141140601
2	TCF12	chr3:141139909-141141257	A549	lung:	n/a	n/a
3	FOSL2	chr3:141140185-141141046	A549	lung:	n/a	chr3:141140587-141140598 chr3:141140591-141140599 chr3:141140589-141140601
4	POLR2A	chr3:141140257-141140811	GM12878	blood:	n/a	n/a
5	FOXA2	chr3:141140352-141140900	A549	lung:	n/a	n/a
6	POLR2A	chr3:141139916-141141231	IMR90	lung:	n/a	n/a
7	CHD1	chr3:141139813-141141531	IMR90	lung:	n/a	n/a
8	MAX	chr3:141139822-141141070	A549	lung:	n/a	chr3:141140590-141140599
9	RCOR1	chr3:141139787-141141595	IMR90	lung:	n/a	n/a
10	GATA3	chr3:141140155-141141106	A549	lung:	n/a	chr3:141140364-141140375 chr3:141140589-141140598
11	EP300	chr3:141140174-141141004	A549	lung:	n/a	n/a
12	EP300	chr3:141140253-141141037	A549	lung:	n/a	n/a
13	SP1	chr3:141140335-141140929	A549	lung:	n/a	n/a
14	JUND	chr3:141140251-141141144	SK-N-SH	brain:	n/a	chr3:141140587-141140598 chr3:141140591-141140599 chr3:141140589-141140601
15	MAX	chr3:141139999-141140999	A549	lung:	n/a	chr3:141140590-141140599
16	GATA3	chr3:141140338-141141001	SK-N-SH	brain:	n/a	chr3:141140364-141140375 chr3:141140589-141140598
17	JUND	chr3:141140286-141140921	SK-N-SH	brain:	n/a	chr3:141140587-141140598 chr3:141140591-141140599 chr3:141140589-141140601
18	SP1	chr3:141140273-141141030	A549	lung:	n/a	n/a
19	RAD21	chr3:141140307-141141059	A549	lung:	n/a	chr3:141140770-141140779 chr3:141140764-141140783
20	TCF12	chr3:141140360-141140788	A549	lung:	n/a	n/a
21	GATA3	chr3:141140289-141140893	SK-N-SH	brain:	n/a	chr3:141140364-141140375 chr3:141140589-141140598
22	POLR2A	chr3:141140361-141141435	U87	brain:	n/a	n/a
23	TCF12	chr3:141140235-141141034	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:141139030..141141005-chr3:141144023..141146849,2	MCF-7	breast:
2	chr3:141084382..141086475-chr3:141138890..141140900,2	MCF-7	breast:
3	chr3:141134135..141137819-chr3:141137972..141141592,4	K562	blood:
4	chr3:141139559..141142065-chr3:141143518..141146223,2	K562	blood:
5	chr3:141123064..141125479-chr3:141137603..141140380,2	MCF-7	breast:
6	chr3:141138083..141140957-chr3:141173553..141175424,3	MCF-7	breast:
7	chr3:141119769..141122618-chr3:141139415..141144215,5	MCF-7	breast:
8	chr3:141130353..141132401-chr3:141139502..141141974,2	K562	blood:
9	chr3:141134160..141135880-chr3:141139081..141141532,2	MCF-7	breast:

Variant related genes	Relation type
ZBTB38	TF binding region
ENSG00000249417	Chromatin interaction
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13068733	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13077048	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1344672	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1344674	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1346408	0.82[CEU][hapmap]
rs1582874	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1863868	0.82[CEU][hapmap]
rs1991431	1.00[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2871960	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4683605	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4683606	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57345461	0.96[ASN][1000 genomes]
rs58473751	0.96[ASN][1000 genomes]
rs6440003	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440006	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6762826	0.89[JPT][hapmap]
rs6763931	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6764769	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6785012	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6802753	0.83[JPT][hapmap]
rs6808936	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs724016	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7613516	0.81[CEU][hapmap]
rs7624084	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7625643	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7632381	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7650602	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9846396	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9853018	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9856584	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141131600-141144400	Strong transcription	Fetal Intestine Large	intestine
2	chr3:141131600-141145200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:141131800-141144600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:141131800-141161200	Weak transcription	Thymus	Thymus
5	chr3:141132200-141141000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:141132200-141144400	Strong transcription	Fetal Intestine Small	intestine
7	chr3:141132200-141144800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:141132200-141171000	Weak transcription	Primary B cells from cord blood	blood
9	chr3:141133600-141140600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:141133800-141140400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:141133800-141140600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:141133800-141158400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:141133800-141158400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:141134000-141146800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:141134000-141161600	Weak transcription	Fetal Brain Male	brain
16	chr3:141134200-141145200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:141134200-141161600	Weak transcription	Primary T cells from cord blood	blood
18	chr3:141134400-141140600	Weak transcription	Esophagus	oesophagus
19	chr3:141134600-141144400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:141134600-141144600	Weak transcription	Liver	Liver
21	chr3:141134600-141148000	Weak transcription	Brain Germinal Matrix	brain
22	chr3:141134800-141142200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr3:141135200-141144600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:141135400-141144000	Weak transcription	Fetal Kidney	kidney
25	chr3:141135600-141160200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:141136000-141144600	Weak transcription	K562	blood
27	chr3:141136200-141140800	Weak transcription	Fetal Brain Female	brain
28	chr3:141136200-141144600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr3:141136200-141144800	Weak transcription	Colonic Mucosa	Colon
30	chr3:141136400-141142000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:141136400-141144400	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:141136400-141145000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:141137400-141140400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:141137400-141140600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:141137400-141140600	Weak transcription	Gastric	stomach
36	chr3:141137400-141140600	Weak transcription	Pancreas	Pancrea
37	chr3:141137400-141144400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:141137400-141144800	Weak transcription	Stomach Mucosa	stomach
39	chr3:141137600-141144400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:141137600-141146400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:141137800-141140400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:141137800-141142400	Weak transcription	HepG2	liver
43	chr3:141137800-141144800	Weak transcription	HSMMtube	muscle
44	chr3:141138000-141140600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:141138000-141144400	Weak transcription	Fetal Lung	lung
46	chr3:141138000-141152000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:141138200-141140400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:141138200-141140400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:141138200-141140400	Weak transcription	Fetal Stomach	stomach
50	chr3:141138200-141140600	Weak transcription	Right Atrium	heart

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