Variant report

Variant	rs61480659
Chromosome Location	chr2:39665453-39665454
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	CEBPB	chr2:39665167-39665553	A549	lung:	n/a	n/a
2	RCOR1	chr2:39662966-39665554	K562	blood:	n/a	n/a
3	MAX	chr2:39663407-39665631	HCT-116	colon:	n/a	chr2:39665266-39665277 chr2:39665266-39665275 chr2:39665267-39665276 chr2:39665267-39665274
4	CEBPB	chr2:39665089-39665606	Hela-S3	cervix:	n/a	n/a
5	BRCA1	chr2:39664308-39665474	Hela-S3	cervix:	n/a	n/a
6	UBTF	chr2:39662309-39665492	K562	blood:	n/a	n/a
7	MTA3	chr2:39664502-39665520	GM12878	blood:	n/a	n/a
8	USF1	chr2:39664952-39665609	HCT-116	colon:	n/a	chr2:39665266-39665277
9	POLR2A	chr2:39663492-39665476	HepG2	liver:	n/a	n/a
10	CREB1	chr2:39663513-39665577	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:39663595-39665532	Hela-S3	cervix:	n/a	n/a
12	FOS	chr2:39665177-39665659	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr2:39663532-39665508	Hela-S3	cervix:	n/a	n/a
14	MYC	chr2:39665060-39665967	MCF10A-Er-Src	breast:	n/a	chr2:39665266-39665277 chr2:39665266-39665275 chr2:39665267-39665276 chr2:39665267-39665274
15	POLR2A	chr2:39664919-39665460	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr2:39663734-39666027	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr2:39663883-39665533	Hela-S3	cervix:	n/a	n/a
18	STAT3	chr2:39665305-39665495	MCF10A-Er-Src	breast:	n/a	n/a
19	MXI1	chr2:39662210-39666175	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr2:39664867-39665480	GM12891	blood:	n/a	n/a
21	MAX	chr2:39663472-39665636	HepG2	liver:	n/a	chr2:39665266-39665277 chr2:39665266-39665275 chr2:39665267-39665276 chr2:39665267-39665274
22	POLR2A	chr2:39663814-39665976	MCF10A-Er-Src	breast:	n/a	n/a
23	STAT3	chr2:39665074-39665584	MCF10A-Er-Src	breast:	n/a	n/a
24	STAT3	chr2:39665088-39666012	MCF10A-Er-Src	breast:	n/a	n/a
25	MAX	chr2:39663402-39665667	A549	lung:	n/a	chr2:39665266-39665277 chr2:39665266-39665275 chr2:39665267-39665276 chr2:39665267-39665274
26	MAX	chr2:39664820-39665622	K562	blood:	n/a	chr2:39665266-39665277 chr2:39665266-39665275 chr2:39665267-39665276 chr2:39665267-39665274
27	ELF1	chr2:39664803-39665589	MCF-7	breast:	n/a	n/a
28	MAZ	chr2:39663636-39665511	HepG2	liver:	n/a	chr2:39665266-39665277 chr2:39665266-39665275 chr2:39665267-39665276 chr2:39665267-39665274
29	MYC	chr2:39664047-39665609	A549	lung:	n/a	chr2:39665266-39665277 chr2:39665266-39665275 chr2:39665267-39665276 chr2:39665267-39665274
30	TCF12	chr2:39663472-39665510	A549	lung:	n/a	chr2:39665251-39665258
31	FOS	chr2:39665134-39665653	MCF10A-Er-Src	breast:	n/a	n/a
32	MXI1	chr2:39662716-39665699	IMR90	lung:	n/a	n/a
33	POLR2A	chr2:39663728-39665458	MCF-7	breast:	n/a	n/a
34	POLR2A	chr2:39663703-39665500	GM18505	blood:	n/a	n/a
35	MYBL2	chr2:39663567-39665683	HepG2	liver:	n/a	n/a
36	USF1	chr2:39665100-39665471	A549	lung:	n/a	chr2:39665266-39665277
37	POLR2A	chr2:39664925-39665487	GM12891	blood:	n/a	n/a
38	MAX	chr2:39663521-39665581	ECC-1	luminal epithelium:	n/a	chr2:39665266-39665277 chr2:39665266-39665275 chr2:39665267-39665276 chr2:39665267-39665274
39	SIN3AK20	chr2:39665027-39665458	A549	lung:	n/a	n/a
40	POLR2A	chr2:39664071-39665501	GM12878	blood:	n/a	n/a
41	EP300	chr2:39665056-39665798	K562	blood:	n/a	chr2:39665749-39665759
42	USF1	chr2:39665024-39665520	A549	lung:	n/a	chr2:39665266-39665277
43	MAX	chr2:39663416-39665557	A549	lung:	n/a	chr2:39665266-39665277 chr2:39665266-39665275 chr2:39665267-39665276 chr2:39665267-39665274
44	USF2	chr2:39664960-39665574	Hela-S3	cervix:	n/a	n/a
45	GABPA	chr2:39664985-39665489	A549	lung:	n/a	n/a
46	SMC3	chr2:39663642-39665616	Hela-S3	cervix:	n/a	chr2:39664016-39664026
47	POLR2A	chr2:39663580-39665516	HepG2	liver:	n/a	n/a
48	RFX5	chr2:39663553-39665563	Hela-S3	cervix:	n/a	n/a
49	SIN3AK20	chr2:39663032-39665671	MCF-7	breast:	n/a	n/a
50	MAX	chr2:39663495-39665705	HepG2	liver:	n/a	chr2:39665266-39665277 chr2:39665266-39665275 chr2:39665267-39665276 chr2:39665267-39665274

No.	Distal block	Cell Line	Cell type
1	chr2:39603738..39609073-chr2:39660426..39665645,8	MCF-7	breast:
2	chr17:43236605..43238756-chr2:39663829..39665960,2	MCF-7	breast:
3	chr2:39601552..39609752-chr2:39662569..39667062,10	MCF-7	breast:
4	chr2:39664730..39667183-chr2:39678037..39681016,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-4	chr2:39665403-39665454	l_1814_chr2:39518006-39558253_76bGuttman_hLF

Variant related genes	Relation type
MAP4K3	TF binding region
ENSG00000168517	Chromatin interaction
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction
ENSG00000224505	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10196253	1.00[ASN][1000 genomes]
rs11124681	0.94[ASN][1000 genomes]
rs11688998	1.00[ASN][1000 genomes]
rs12623945	1.00[AMR][1000 genomes]
rs17023504	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17023656	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17023777	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3755170	1.00[AMR][1000 genomes]
rs3755175	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3770676	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3770677	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3770679	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs55748017	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56833014	1.00[ASN][1000 genomes]
rs57103739	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57232122	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs58704884	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59784621	1.00[AMR][1000 genomes]
rs60192971	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6544226	0.94[ASN][1000 genomes]
rs7591102	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39661000-39666000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:39661800-39667000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:39661800-39667000	Active TSS	Aorta	Aorta
4	chr2:39662000-39665600	Active TSS	Right Ventricle	heart
5	chr2:39662000-39665800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr2:39662000-39666000	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr2:39662000-39666200	Active TSS	Ovary	ovary
8	chr2:39662200-39665600	Active TSS	Fetal Muscle Trunk	muscle
9	chr2:39662400-39665600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr2:39662400-39665600	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr2:39662400-39665600	Active TSS	Lung	lung
12	chr2:39662400-39665600	Active TSS	NHDF-Ad	bronchial
13	chr2:39662400-39666000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:39662600-39665600	Active TSS	Brain Substantia Nigra	brain
15	chr2:39662600-39665600	Active TSS	Psoas Muscle	Psoas
16	chr2:39662600-39665600	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr2:39662600-39666000	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr2:39662600-39666000	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr2:39662800-39665600	Active TSS	Left Ventricle	heart
20	chr2:39662800-39665600	Active TSS	Pancreas	Pancrea
21	chr2:39663000-39665800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:39663000-39666000	Active TSS	Colon Smooth Muscle	Colon
23	chr2:39663200-39665600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:39663200-39665600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:39663400-39665600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr2:39663400-39665600	Active TSS	Thymus	Thymus
27	chr2:39663600-39666000	Active TSS	Duodenum Mucosa	Duodenum
28	chr2:39664000-39665600	Active TSS	Fetal Brain Female	brain
29	chr2:39664600-39665600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:39664600-39665800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr2:39664600-39665800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr2:39664800-39665600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr2:39664800-39665600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr2:39664800-39665600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr2:39664800-39665600	Flanking Active TSS	Fetal Brain Male	brain
36	chr2:39664800-39665600	Flanking Active TSS	Dnd41	blood
37	chr2:39664800-39665600	Flanking Active TSS	HUVEC	blood vessel
38	chr2:39664800-39665600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr2:39664800-39665600	Flanking Active TSS	NH-A	brain
40	chr2:39664800-39665800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:39664800-39667000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:39665000-39665600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:39665000-39665600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:39665000-39665600	Flanking Active TSS	Brain Angular Gyrus	brain
45	chr2:39665000-39665600	Flanking Active TSS	Fetal Heart	heart
46	chr2:39665000-39665600	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr2:39665000-39665600	Flanking Active TSS	Placenta	Placenta
48	chr2:39665000-39665600	Flanking Active TSS	HMEC	breast
49	chr2:39665000-39665600	Flanking Active TSS	K562	blood
50	chr2:39665000-39665600	Flanking Active TSS	NHEK	skin

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