Variant report

Variant	rs2278781
Chromosome Location	chr3:119042306-119042307
allele	A/C
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	EP300	chr3:119041781-119042646	GM12878	blood:	n/a	chr3:119041973-119041987 chr3:119042149-119042165 chr3:119041956-119041972
2	POLR2A	chr3:119041212-119042480	GM18951	blood:	n/a	n/a
3	TCF3	chr3:119041664-119042320	GM12878	blood:	n/a	n/a
4	IKZF1	chr3:119041801-119042634	GM12878	blood:	n/a	n/a
5	ETS1	chr3:119041611-119042352	GM12878	blood:	n/a	chr3:119042196-119042213 chr3:119041680-119041691 chr3:119041791-119041802
6	ZEB1	chr3:119041941-119042644	GM12878	blood:	n/a	chr3:119042450-119042457 chr3:119042467-119042474 chr3:119041970-119041978
7	RELA	chr3:119041704-119042771	GM19099	blood:	n/a	chr3:119042019-119042028 chr3:119042019-119042028
8	POLR2A	chr3:119040718-119042639	IMR90	lung:	n/a	n/a
9	MYC	chr3:119041317-119042420	NB4	blood:	n/a	chr3:119042031-119042041
10	JUND	chr3:119041478-119042397	K562	blood:	n/a	chr3:119042065-119042075 chr3:119042065-119042075 chr3:119041798-119041807 chr3:119042066-119042074 chr3:119042065-119042075
11	ZNF263	chr3:119041262-119042548	HEK293-T-REx	kidney:	n/a	chr3:119041626-119041635
12	ZNF384	chr3:119041887-119042472	K562	blood:	n/a	n/a
13	MAX	chr3:119042259-119042587	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr3:119041682-119042323	A549	lung:	n/a	chr3:119042031-119042041
15	MAX	chr3:119041694-119042551	GM12878	blood:	n/a	chr3:119042031-119042041
16	ATF2	chr3:119041645-119042605	GM12878	blood:	n/a	n/a
17	ZNF143	chr3:119041582-119042398	GM12878	blood:	n/a	chr3:119041792-119041802
18	YY1	chr3:119041667-119042595	GM12891	blood:	n/a	chr3:119041719-119041728 chr3:119042153-119042167 chr3:119042080-119042094 chr3:119042024-119042038 chr3:119042081-119042095 chr3:119041788-119041799
19	ZBTB7A	chr3:119041279-119042418	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr3:119041260-119042608	GM18526	blood:	n/a	n/a
21	NFIC	chr3:119041685-119042531	GM12878	blood:	n/a	n/a
22	RELA	chr3:119041715-119042803	GM10847	blood:	n/a	chr3:119042019-119042028 chr3:119042019-119042028
23	EP300	chr3:119041789-119042352	GM12878	blood:	n/a	chr3:119041973-119041987 chr3:119042149-119042165 chr3:119041956-119041972
24	MEF2C	chr3:119041731-119042337	GM12878	blood:	n/a	n/a
25	RELA	chr3:119040978-119042718	GM15510	blood:	n/a	chr3:119042019-119042028 chr3:119042019-119042028
26	RFX5	chr3:119041869-119042311	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:119041191-119042416	PANC-1	pancreas:	n/a	n/a
28	ELF1	chr3:119041161-119042626	GM12878	blood:	n/a	n/a
29	HDAC2	chr3:119041657-119042410	MCF-7	breast:	n/a	chr3:119042083-119042092
30	USF2	chr3:119042270-119042560	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:119041160-119042349	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:119041349-119042635	MCF-7	breast:	n/a	n/a
33	POLR2A	chr3:119040800-119042455	GM12878	blood:	n/a	n/a
34	EBF1	chr3:119041811-119042430	GM12878	blood:	n/a	n/a
35	EP300	chr3:119041862-119042420	GM12878	blood:	n/a	chr3:119041973-119041987 chr3:119042149-119042165 chr3:119041956-119041972
36	TAF1	chr3:119041588-119042340	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr3:119041099-119042674	GM12892	blood:	n/a	n/a
38	RELA	chr3:119041792-119042608	GM18951	blood:	n/a	chr3:119042019-119042028 chr3:119042019-119042028
39	POLR2A	chr3:119041228-119042384	MCF-7	breast:	n/a	n/a
40	STAT1	chr3:119041738-119042519	Hela-S3	cervix:	n/a	chr3:119042040-119042051 chr3:119042042-119042050 chr3:119042036-119042056 chr3:119042042-119042051 chr3:119042041-119042050
41	USF2	chr3:119042263-119042634	H1-hESC	embryonic stem cell:	n/a	n/a
42	TCF7L2	chr3:119041474-119042343	HCT-116	colon:	n/a	n/a
43	POLR2A	chr3:119041010-119042487	GM12878	blood:	n/a	n/a
44	TCF12	chr3:119041380-119042426	A549	lung:	n/a	chr3:119041646-119041656
45	POLR2A	chr3:119041124-119042804	GM12891	blood:	n/a	n/a
46	TCF12	chr3:119041764-119042307	GM12878	blood:	n/a	n/a
47	POLR2A	chr3:119041112-119042314	HUVEC	blood vessel:	n/a	n/a
48	TBL1XR1	chr3:119041725-119042460	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:119041739-119042312	Hela-S3	cervix:	n/a	n/a
50	POU2F2	chr3:119041194-119042536	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:119040381..119043387-chr3:119393976..119396207,3	K562	blood:
2	chr3:119039655..119042714-chr3:119058706..119061390,3	MCF-7	breast:
3	chr3:119016211..119028042-chr3:119037960..119043695,12	MCF-7	breast:
4	chr3:119041713..119043287-chr3:119530571..119533210,2	MCF-7	breast:
5	chr3:119012312..119014941-chr3:119040203..119043471,4	MCF-7	breast:
6	chr3:119011662..119015799-chr3:119040784..119043293,4	MCF-7	breast:
7	chr3:119041710..119043371-chr3:119051543..119054199,2	K562	blood:
8	chr3:119040625..119043456-chr3:119181021..119182647,3	MCF-7	breast:
9	chr3:119040520..119043561-chr3:119060040..119062334,3	MCF-7	breast:

Variant related genes	Relation type
ARHGAP31-AS1	TF binding region
ARHGAP31	TF binding region
ENSG00000176142	Chromatin interaction
ENSG00000031081	Chromatin interaction
ENSG00000207310	Chromatin interaction
ENSG00000138495	Chromatin interaction
ENSG00000242829	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10511386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934490	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12497738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13314464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1375135	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1448434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687994	0.86[EUR][1000 genomes]
rs58568360	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62265236	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62265237	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6438518	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6438519	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6438520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438522	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6438523	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762580	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6785727	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6786522	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6789881	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6799733	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7610546	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7611832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7619210	0.85[EUR][1000 genomes]
rs7644570	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7649480	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7649930	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9822211	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9825078	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9834750	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9847963	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9861372	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9861688	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9877740	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829694	chr3:119011488-119153579	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119040600-119042400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:119040600-119042400	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:119040600-119042600	Flanking Active TSS	HUVEC	blood vessel
4	chr3:119040600-119043000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr3:119040600-119043000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr3:119040800-119042400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:119040800-119042400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:119040800-119042600	Flanking Active TSS	Dnd41	blood
9	chr3:119040800-119042800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr3:119041000-119042400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:119041000-119042400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:119041000-119042400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:119041000-119042400	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr3:119041000-119042400	Active TSS	Brain Germinal Matrix	brain
15	chr3:119041000-119042400	Active TSS	Brain Substantia Nigra	brain
16	chr3:119041000-119042400	Active TSS	Colon Smooth Muscle	Colon
17	chr3:119041000-119042400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr3:119041000-119042400	Active TSS	Fetal Intestine Large	intestine
19	chr3:119041000-119042400	Active TSS	Fetal Lung	lung
20	chr3:119041000-119042400	Active TSS	NHLF	lung
21	chr3:119041000-119042600	Active TSS	H9 Cell Line	embryonic stem cell
22	chr3:119041000-119042600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:119041000-119042600	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr3:119041000-119042800	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr3:119041000-119042800	Active TSS	K562	blood
26	chr3:119041200-119042400	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr3:119041200-119042400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:119041200-119042400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:119041200-119042400	Active TSS	Aorta	Aorta
30	chr3:119041200-119042400	Active TSS	Liver	Liver
31	chr3:119041200-119042400	Active TSS	Brain Cingulate Gyrus	brain
32	chr3:119041200-119042400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:119041200-119042400	Active TSS	Left Ventricle	heart
34	chr3:119041200-119042400	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr3:119041200-119042400	Active TSS	Spleen	Spleen
36	chr3:119041200-119042400	Active TSS	Hela-S3	cervix
37	chr3:119041200-119042600	Active TSS	Ovary	ovary
38	chr3:119041200-119042800	Active TSS	Fetal Kidney	kidney
39	chr3:119041200-119042800	Flanking Active TSS	HMEC	breast
40	chr3:119041400-119042400	Active TSS	H1 Cell Line	embryonic stem cell
41	chr3:119041400-119042400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:119041400-119042400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:119041400-119042400	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr3:119041400-119042400	Active TSS	Brain Angular Gyrus	brain
45	chr3:119041400-119042400	Active TSS	Brain Anterior Caudate	brain
46	chr3:119041400-119042400	Active TSS	Fetal Stomach	stomach
47	chr3:119041400-119042400	Active TSS	Gastric	stomach
48	chr3:119041400-119042400	Active TSS	Placenta Amnion	Placenta Amnion
49	chr3:119041400-119042400	Active TSS	Psoas Muscle	Psoas
50	chr3:119041400-119042400	Active TSS	A549	lung

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