Variant report

Variant	rs4047262
Chromosome Location	chr2:234474438-234474439
allele	A/C/G
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	chr2:234474254-234475647	HepG2	liver:	n/a	n/a
2	BHLHE40	chr2:234474372-234474782	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:234474394-234475654	HCT-116	colon:	n/a	n/a
4	STAT3	chr2:234474212-234474562	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:234474373-234475708	U87	brain:	n/a	n/a
6	ZNF143	chr2:234474219-234474468	GM12878	blood:	n/a	n/a
7	ZNF384	chr2:234474278-234475218	GM12878	blood:	n/a	n/a
8	CHD2	chr2:234474405-234475666	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr2:234474265-234475656	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr2:234474387-234475589	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:234474311-234475729	GM18951	blood:	n/a	n/a
12	ZNF384	chr2:234474322-234474739	K562	blood:	n/a	n/a
13	POLR2A	chr2:234474416-234475731	GM19099	blood:	n/a	n/a
14	MAZ	chr2:234474428-234475653	K562	blood:	n/a	chr2:234474801-234474811
15	SIN3A	chr2:234474285-234475629	H1-hESC	embryonic stem cell:	n/a	n/a
16	TBP	chr2:234474237-234475560	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:234472877-234475700	MCF10A-Er-Src	breast:	n/a	n/a
18	MAZ	chr2:234474285-234475646	IMR90	lung:	n/a	chr2:234474801-234474811
19	BCL3	chr2:234474395-234475621	A549	lung:	n/a	chr2:234475543-234475556 chr2:234474817-234474826 chr2:234475463-234475476
20	POLR2A	chr2:234474267-234475696	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr2:234473069-234475737	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr2:234474273-234474579	MCF-7	breast:	n/a	n/a
23	HEY1	chr2:234474426-234475858	HepG2	liver:	n/a	chr2:234475308-234475323 chr2:234475462-234475477 chr2:234475464-234475479
24	TBP	chr2:234474301-234475724	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr2:234474294-234475610	HepG2	liver:	n/a	n/a
26	TCF12	chr2:234474173-234475716	A549	lung:	n/a	n/a
27	MAX	chr2:234474269-234475689	A549	lung:	n/a	chr2:234474801-234474811
28	POLR2A	chr2:234474255-234475695	HUVEC	blood vessel:	n/a	n/a
29	MYBL2	chr2:234474382-234475673	HepG2	liver:	n/a	n/a
30	POLR2A	chr2:234473396-234475545	K562	blood:	n/a	n/a
31	TBL1XR1	chr2:234474369-234474659	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:234474400-234475658	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr2:234474392-234475691	GM12878	blood:	n/a	n/a
34	HCFC1	chr2:234474337-234475669	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr2:234474287-234475685	GM12891	blood:	n/a	n/a
36	POLR2A	chr2:234474379-234475774	U87	brain:	n/a	n/a
37	MAZ	chr2:234474267-234475639	HepG2	liver:	n/a	chr2:234474801-234474811

No.	Distal block	Cell Line	Cell type
1	chr2:234452682..234455147-chr2:234473464..234475374,2	MCF-7	breast:
2	chr2:234473931..234475939-chr2:234762064..234763860,2	K562	blood:
3	chr2:234473282..234477495-chr2:234598048..234603332,9	MCF-7	breast:
4	chr2:234474046..234476375-chr2:234618981..234621894,3	MCF-7	breast:
5	chr2:234400872..234402381-chr2:234473582..234476254,2	MCF-7	breast:
6	chr2:234393753..234400835-chr2:234472864..234476478,8	MCF-7	breast:
7	chr2:234389092..234391362-chr2:234473035..234476486,3	MCF-7	breast:
8	chr2:234472037..234477650-chr2:234599067..234602356,8	MCF-7	breast:

Variant related genes	Relation type
USP40	TF binding region
ENSG00000085982	Chromatin interaction
ENSG00000240224	Chromatin interaction
ENSG00000123485	Chromatin interaction
ENSG00000271639	Chromatin interaction
ENSG00000167165	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs28968505	0.88[AFR][1000 genomes]
rs4281901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4392254	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4588184	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55888324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56274731	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56306918	1.00[AMR][1000 genomes]
rs56317380	1.00[AMR][1000 genomes]
rs57285092	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57768657	0.88[AFR][1000 genomes]
rs58330864	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58489211	1.00[AMR][1000 genomes]
rs58583213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58864422	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59543173	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59954119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61376069	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6726032	1.00[AMR][1000 genomes]
rs6734355	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995922	1.00[AMR][1000 genomes]
rs73995923	1.00[AMR][1000 genomes]
rs73995944	1.00[AMR][1000 genomes]
rs73995946	1.00[AMR][1000 genomes]
rs73995947	1.00[AMR][1000 genomes]
rs73995948	1.00[AMR][1000 genomes]
rs73995949	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995950	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995970	1.00[AMR][1000 genomes]
rs73995972	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995973	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995974	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73995980	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996001	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996105	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73996138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997606	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997607	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997608	1.00[AMR][1000 genomes]
rs73997611	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997612	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997630	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997631	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997633	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997637	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73997638	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs745154	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7580191	1.00[AMR][1000 genomes]
rs7584192	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7593807	1.00[AMR][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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv519876	chr2:234466843-234493048	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234432200-234474800	Weak transcription	Spleen	Spleen
2	chr2:234441600-234474800	Weak transcription	Gastric	stomach
3	chr2:234447800-234474800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:234466000-234474600	Weak transcription	Pancreas	Pancrea
5	chr2:234466400-234474800	Weak transcription	Esophagus	oesophagus
6	chr2:234466600-234474800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:234469800-234474600	Weak transcription	Placenta	Placenta
8	chr2:234473200-234474600	Weak transcription	Left Ventricle	heart
9	chr2:234473800-234474600	Enhancers	Fetal Brain Female	brain
10	chr2:234473800-234474600	Flanking Active TSS	A549	lung
11	chr2:234474000-234474600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:234474000-234474600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:234474000-234474600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:234474000-234474600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:234474000-234474600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr2:234474000-234474600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr2:234474000-234474600	Flanking Active TSS	Hela-S3	cervix
18	chr2:234474000-234474600	Flanking Active TSS	HMEC	breast
19	chr2:234474000-234474600	Flanking Active TSS	NHEK	skin
20	chr2:234474000-234474600	Flanking Active TSS	Osteobl	bone
21	chr2:234474000-234474800	Flanking Active TSS	Dnd41	blood
22	chr2:234474000-234475600	Active TSS	Fetal Brain Male	brain
23	chr2:234474000-234475800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:234474000-234475800	Active TSS	Right Atrium	heart
25	chr2:234474000-234475800	Active TSS	Stomach Smooth Muscle	stomach
26	chr2:234474200-234474600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:234474200-234474600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr2:234474200-234474600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr2:234474200-234474600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr2:234474200-234474600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr2:234474200-234474600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr2:234474200-234474600	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr2:234474200-234474600	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr2:234474200-234474600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr2:234474200-234474600	Flanking Active TSS	Fetal Kidney	kidney
36	chr2:234474200-234474600	Flanking Active TSS	Fetal Lung	lung
37	chr2:234474200-234474600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr2:234474200-234474600	Flanking Active TSS	NH-A	brain
39	chr2:234474200-234474600	Flanking Active TSS	NHDF-Ad	bronchial
40	chr2:234474200-234474600	Flanking Active TSS	NHLF	lung
41	chr2:234474200-234474800	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr2:234474200-234474800	Active TSS	Primary B cells from cord blood	blood
43	chr2:234474200-234474800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr2:234474200-234475000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:234474200-234475200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:234474200-234475400	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr2:234474200-234475600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:234474200-234475600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:234474200-234475800	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr2:234474200-234475800	Active TSS	iPS-15b Cell Line	embryonic stem cell

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