Variant report

Variant	rs60192971
Chromosome Location	chr2:39663261-39663262
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	RCOR1	chr2:39662966-39665554	K562	blood:	n/a	n/a
2	NFIC	chr2:39662997-39663460	SK-N-SH	brain:	n/a	n/a
3	SIN3A	chr2:39663124-39665275	H1-hESC	embryonic stem cell:	n/a	chr2:39664207-39664220
4	REST	chr2:39663223-39665181	H1-neurons	neurons:	n/a	chr2:39664865-39664878 chr2:39664436-39664449
5	UBTF	chr2:39662309-39665492	K562	blood:	n/a	n/a
6	HNF4A	chr2:39663115-39663510	HepG2	liver:	n/a	chr2:39663333-39663341 chr2:39663335-39663347 chr2:39663333-39663348 chr2:39663333-39663348 chr2:39663333-39663348 chr2:39663334-39663342 chr2:39663333-39663348 chr2:39663334-39663346 chr2:39663333-39663348 chr2:39663333-39663348
7	HNF4A	chr2:39663093-39663495	HepG2	liver:	n/a	chr2:39663333-39663341 chr2:39663335-39663347 chr2:39663333-39663348 chr2:39663333-39663348 chr2:39663333-39663348 chr2:39663334-39663342 chr2:39663333-39663348 chr2:39663334-39663346 chr2:39663333-39663348 chr2:39663333-39663348
8	RAD21	chr2:39663099-39663395	SK-N-SH_RA	brain:	n/a	n/a
9	MXI1	chr2:39662210-39666175	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr2:39662942-39664019	HepG2	liver:	n/a	n/a
11	EP300	chr2:39662989-39663406	SK-N-SH_RA	brain:	n/a	n/a
12	MBD4	chr2:39663034-39664116	HepG2	liver:	n/a	n/a
13	MXI1	chr2:39662716-39665699	IMR90	lung:	n/a	n/a
14	UBTF	chr2:39663106-39664795	K562	blood:	n/a	n/a
15	RAD21	chr2:39663120-39664635	A549	lung:	n/a	n/a
16	POLR2A	chr2:39663181-39664839	IMR90	lung:	n/a	n/a
17	SIN3AK20	chr2:39663032-39665671	MCF-7	breast:	n/a	n/a
18	PBX3	chr2:39662922-39663565	SK-N-SH	brain:	n/a	n/a
19	EP300	chr2:39663060-39663369	SK-N-SH_RA	brain:	n/a	n/a
20	MAX	chr2:39663137-39665681	Hela-S3	cervix:	n/a	chr2:39665266-39665277 chr2:39665266-39665275 chr2:39665267-39665276 chr2:39665267-39665274
21	SIN3AK20	chr2:39663107-39663473	SK-N-SH	brain:	n/a	n/a
22	PBX3	chr2:39662951-39663877	SK-N-SH	brain:	n/a	n/a
23	CEBPB	chr2:39663131-39663300	K562	blood:	n/a	n/a
24	RAD21	chr2:39663099-39665353	IMR90	lung:	n/a	chr2:39665045-39665057
25	USF2	chr2:39663201-39663366	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:39662921-39665454	HepG2	liver:	n/a	n/a
27	USF2	chr2:39663203-39663311	Hela-S3	cervix:	n/a	n/a
28	ZNF263	chr2:39662245-39665558	HEK293-T-REx	kidney:	n/a	chr2:39664436-39664445 chr2:39664470-39664479 chr2:39663909-39663918 chr2:39664443-39664464 chr2:39664471-39664492
29	MBD4	chr2:39662790-39663963	HepG2	liver:	n/a	n/a
30	HDAC2	chr2:39663135-39664795	HepG2	liver:	n/a	chr2:39663459-39663473 chr2:39663334-39663342 chr2:39663463-39663477 chr2:39663460-39663474
31	HNF4A	chr2:39663184-39665428	HepG2	liver:	n/a	chr2:39663333-39663341 chr2:39663335-39663347 chr2:39663333-39663348 chr2:39663333-39663348 chr2:39663333-39663348 chr2:39664756-39664768 chr2:39663334-39663342 chr2:39663333-39663348 chr2:39664755-39664768 chr2:39663865-39663873 chr2:39663334-39663346 chr2:39663333-39663348 chr2:39664755-39664763 chr2:39663333-39663348
32	RAD21	chr2:39663090-39663367	SK-N-SH_RA	brain:	n/a	n/a
33	MYC	chr2:39663243-39665475	K562	blood:	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	chr2:39662097..39664715-chr2:39993095..39995663,2	K562	blood:
3	chr2:39601552..39609752-chr2:39662569..39667062,10	MCF-7	breast:
4	chr2:39661305..39663930-chr2:39740460..39742003,2	MCF-7	breast:
5	chr2:39619324..39621910-chr2:39662875..39665257,2	K562	blood:

Variant related genes	Relation type
ENSG00000231312	TF binding region
ENSG00000231312	Chromatin interaction
ENSG00000011566	Chromatin interaction
ENSG00000252239	Chromatin interaction
ENSG00000138050	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]
rs61480659	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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39659200-39663400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr2:39660000-39663400	Flanking Active TSS	K562	blood
3	chr2:39661000-39666000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:39661200-39665000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:39661400-39663400	Flanking Active TSS	Fetal Brain Female	brain
6	chr2:39661400-39664000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr2:39661400-39665000	Active TSS	Right Atrium	heart
8	chr2:39661600-39663400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:39661600-39663400	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr2:39661600-39663400	Flanking Active TSS	Hela-S3	cervix
11	chr2:39661600-39663600	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr2:39661600-39663800	Flanking Active TSS	Dnd41	blood
13	chr2:39661800-39663600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr2:39661800-39664000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:39661800-39665200	Active TSS	HSMMtube	muscle
16	chr2:39661800-39667000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:39661800-39667000	Active TSS	Aorta	Aorta
18	chr2:39662000-39663600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:39662000-39665000	Active TSS	Stomach Smooth Muscle	stomach
20	chr2:39662000-39665200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:39662000-39665200	Active TSS	NHLF	lung
22	chr2:39662000-39665400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:39662000-39665400	Active TSS	HSMM	muscle
24	chr2:39662000-39665600	Active TSS	Right Ventricle	heart
25	chr2:39662000-39665800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr2:39662000-39666000	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr2:39662000-39666200	Active TSS	Ovary	ovary
28	chr2:39662200-39663400	Flanking Active TSS	HUVEC	blood vessel
29	chr2:39662200-39663800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:39662200-39663800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr2:39662200-39663800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr2:39662200-39665600	Active TSS	Fetal Muscle Trunk	muscle
33	chr2:39662400-39663400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr2:39662400-39663400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:39662400-39663400	Flanking Active TSS	Liver	Liver
36	chr2:39662400-39663800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:39662400-39664000	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr2:39662400-39664000	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr2:39662400-39664000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr2:39662400-39664800	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr2:39662400-39665200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr2:39662400-39665200	Active TSS	H9 Cell Line	embryonic stem cell
43	chr2:39662400-39665200	Active TSS	Brain Hippocampus Middle	brain
44	chr2:39662400-39665200	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr2:39662400-39665200	Bivalent/Poised TSS	HepG2	liver
46	chr2:39662400-39665400	Active TSS	Colonic Mucosa	Colon
47	chr2:39662400-39665600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr2:39662400-39665600	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr2:39662400-39665600	Active TSS	Lung	lung
50	chr2:39662400-39665600	Active TSS	NHDF-Ad	bronchial

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