Variant report

Variant	rs622954
Chromosome Location	chr2:234763225-234763226
allele	A/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	PML	chr2:234762856-234763735	GM12878	blood:	n/a	n/a
2	FOXA1	chr2:234762928-234763658	HepG2	liver:	n/a	n/a
3	SP1	chr2:234763044-234763581	GM12878	blood:	n/a	chr2:234763215-234763227 chr2:234763338-234763348 chr2:234763338-234763348 chr2:234763236-234763257 chr2:234763215-234763226
4	RUNX3	chr2:234763212-234763667	GM12878	blood:	n/a	n/a
5	FOXM1	chr2:234762589-234763888	ECC-1	luminal epithelium:	n/a	n/a
6	SP1	chr2:234762785-234763935	HCT-116	colon:	n/a	chr2:234763215-234763227 chr2:234763338-234763348 chr2:234763338-234763348 chr2:234762872-234762886 chr2:234763236-234763257 chr2:234763215-234763226
7	YY1	chr2:234762850-234763674	ECC-1	luminal epithelium:	n/a	chr2:234763557-234763566
8	STAT5A	chr2:234763194-234763706	K562	blood:	n/a	n/a
9	POLR2A	chr2:234762944-234764240	IMR90	lung:	n/a	n/a
10	HEY1	chr2:234762887-234763664	HepG2	liver:	n/a	n/a
11	MXI1	chr2:234762986-234763867	GM12878	blood:	n/a	n/a
12	GABPA	chr2:234763037-234763757	HL-60	blood:	n/a	n/a
13	BHLHE40	chr2:234763075-234763510	HepG2	liver:	n/a	n/a
14	ELK4	chr2:234763171-234763902	Hela-S3	cervix:	n/a	n/a
15	GATA1	chr2:234762999-234764180	PBDE	blood:	n/a	chr2:234763473-234763490
16	MXI1	chr2:234762958-234763625	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr2:234762797-234763716	GM12878	blood:	n/a	n/a
18	YY1	chr2:234762926-234763605	ECC-1	luminal epithelium:	n/a	chr2:234763557-234763566
19	NFIC	chr2:234763032-234763532	HepG2	liver:	n/a	n/a
20	NFIC	chr2:234762928-234763614	HepG2	liver:	n/a	n/a
21	SP1	chr2:234763132-234763445	K562	blood:	n/a	chr2:234763215-234763227 chr2:234763338-234763348 chr2:234763338-234763348 chr2:234763236-234763257 chr2:234763215-234763226
22	ELF1	chr2:234762412-234763621	GM12878	blood:	n/a	chr2:234763377-234763389 chr2:234763017-234763029
23	POLR2A	chr2:234762824-234763828	ProgFib	skin:	n/a	n/a
24	POLR2A	chr2:234762579-234763667	GM10847	blood:	n/a	n/a
25	NFYA	chr2:234763081-234763485	GM12878	blood:	n/a	chr2:234763311-234763329
26	MAX	chr2:234762991-234763669	SK-N-SH	brain:	n/a	n/a
27	SIN3AK20	chr2:234762848-234763523	K562	blood:	n/a	n/a
28	MAX	chr2:234762877-234763717	MCF-7	breast:	n/a	n/a
29	CREB1	chr2:234762828-234763647	A549	lung:	n/a	n/a
30	JUND	chr2:234763140-234763648	A549	lung:	n/a	n/a
31	POLR2A	chr2:234762585-234763642	NB4	blood:	n/a	n/a
32	CHD1	chr2:234762894-234763612	GM12878	blood:	n/a	n/a
33	SP1	chr2:234762914-234763574	H1-hESC	embryonic stem cell:	n/a	chr2:234763215-234763227 chr2:234763338-234763348 chr2:234763338-234763348 chr2:234763236-234763257 chr2:234763215-234763226
34	E2F4	chr2:234760995-234764094	MCF10A-Er-Src	breast:	n/a	chr2:234762623-234762633
35	FOSL2	chr2:234762960-234763925	A549	lung:	n/a	n/a
36	POLR2A	chr2:234762905-234763613	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr2:234762952-234763666	K562	blood:	n/a	n/a
38	ELF1	chr2:234762984-234763592	K562	blood:	n/a	chr2:234763377-234763389 chr2:234763017-234763029
39	CEBPB	chr2:234762943-234763732	A549	lung:	n/a	n/a
40	MXI1	chr2:234761711-234763997	IMR90	lung:	n/a	n/a
41	MAX	chr2:234761813-234763874	A549	lung:	n/a	n/a
42	KAP1	chr2:234763207-234763865	U2OS	brain:	n/a	n/a
43	CBX3	chr2:234763144-234763777	K562	blood:	n/a	n/a
44	POLR2A	chr2:234762781-234763703	HCT-116	colon:	n/a	n/a
45	MAX	chr2:234763043-234763262	K562	blood:	n/a	n/a
46	SIN3AK20	chr2:234762874-234763861	A549	lung:	n/a	n/a
47	TAF1	chr2:234762764-234763876	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr2:234762840-234763619	GM12892	blood:	n/a	n/a
49	POLR2A	chr2:234762975-234763621	SK-N-SH	brain:	n/a	n/a
50	RUNX3	chr2:234762961-234763673	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234762685..234763322-chr22:37595016..37595706,2	NB4	blood:
2	chr2:234762991..234763952-chr6:26043968..26044562,2	Hela-S3	cervix:
3	chr2:234761504..234764477-chr2:234824983..234827662,2	MCF-7	breast:
4	chr2:234760939..234763453-chr2:235403879..235406192,2	K562	blood:
5	chr1:192778136..192778641-chr2:234762703..234763332,2	Hela-S3	cervix:
6	chr2:234473931..234475939-chr2:234762064..234763860,2	K562	blood:
7	chr2:233739634..233741752-chr2:234762062..234763820,2	MCF-7	breast:

Variant related genes	Relation type
HJURP	TF binding region
ENSG00000085982	Chromatin interaction
ENSG00000188042	Chromatin interaction
ENSG00000116741	Chromatin interaction
ENSG00000234816	Chromatin interaction
ENSG00000182600	Chromatin interaction
ENSG00000144481	Chromatin interaction
ENSG00000133466	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11562979	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11563228	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13390819	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13398248	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13403318	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13406453	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13406457	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13410024	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13410032	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17862907	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17862921	0.83[ASN][1000 genomes]
rs17863825	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17863826	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17863838	0.87[ASN][1000 genomes]
rs17864729	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17868368	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17868369	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs186159	0.93[ASN][1000 genomes]
rs188492	0.93[ASN][1000 genomes]
rs213541	0.93[ASN][1000 genomes]
rs213543	0.93[ASN][1000 genomes]
rs213544	0.93[ASN][1000 genomes]
rs213550	0.93[ASN][1000 genomes]
rs213556	0.86[AMR][1000 genomes]
rs2173746	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2173747	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2530796	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2650888	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs473504	0.82[AMR][1000 genomes]
rs494812	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs498680	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs498696	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs498786	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs498790	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs499703	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs501650	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs502321	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs506632	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs511387	0.93[ASN][1000 genomes]
rs531771	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs566985	0.93[ASN][1000 genomes]
rs568906	0.93[ASN][1000 genomes]
rs570800	0.93[ASN][1000 genomes]
rs575194	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs577734	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs577782	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs577820	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs579327	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs581377	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs596509	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs598759	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs598760	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs611131	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs611169	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs611563	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs625151	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs628138	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs657658	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs658054	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs658607	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs672831	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6741751	0.87[ASN][1000 genomes]
rs686003	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs686007	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs686802	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs688677	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9646718	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 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	chr2:234761200-234763600	Active TSS	NHLF	lung
2	chr2:234761200-234764000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:234761400-234763800	Active TSS	NHDF-Ad	bronchial
4	chr2:234761400-234764000	Active TSS	H1 Cell Line	embryonic stem cell
5	chr2:234761600-234763600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:234761600-234763600	Active TSS	Hela-S3	cervix
7	chr2:234761600-234763800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr2:234761600-234763800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:234761600-234763800	Active TSS	Fetal Kidney	kidney
10	chr2:234761600-234763800	Active TSS	GM12878-XiMat	blood
11	chr2:234761800-234763400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:234761800-234763600	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr2:234761800-234763800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:234761800-234763800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:234761800-234763800	Active TSS	Fetal Intestine Small	intestine
16	chr2:234761800-234763800	Active TSS	Rectal Smooth Muscle	rectum
17	chr2:234761800-234764000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:234761800-234764000	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr2:234762000-234763600	Active TSS	Esophagus	oesophagus
20	chr2:234762000-234763800	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr2:234762000-234763800	Active TSS	Fetal Intestine Large	intestine
22	chr2:234762000-234763800	Active TSS	HSMM	muscle
23	chr2:234762000-234764000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:234762000-234764000	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr2:234762200-234763400	Bivalent/Poised TSS	HepG2	liver
26	chr2:234762200-234763400	Active TSS	NHEK	skin
27	chr2:234762200-234763600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:234762200-234763600	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr2:234762200-234763600	Active TSS	Muscle Satellite Cultured Cells	--
30	chr2:234762200-234763800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:234762200-234763800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:234762200-234763800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:234762200-234764000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr2:234762200-234764000	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr2:234762400-234763400	Active TSS	HMEC	breast
36	chr2:234762400-234763600	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr2:234762400-234763600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:234762400-234763600	Active TSS	Small Intestine	intestine
39	chr2:234762400-234763600	Active TSS	K562	blood
40	chr2:234762400-234763600	Active TSS	Osteobl	bone
41	chr2:234762400-234763800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:234762400-234763800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:234762400-234763800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:234762400-234763800	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr2:234762400-234763800	Active TSS	Brain Substantia Nigra	brain
46	chr2:234762400-234763800	Active TSS	HSMMtube	muscle
47	chr2:234762400-234764200	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr2:234762400-234764600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:234762600-234763400	Enhancers	Fetal Brain Male	brain
50	chr2:234762600-234763400	Active TSS	Dnd41	blood

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