Variant report

Variant	rs2271218
Chromosome Location	chr5:98110531-98110532
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	SIN3AK20	chr5:98108522-98110761	SK-N-SH	brain:	n/a	n/a
2	FOXA2	chr5:98109862-98110612	A549	lung:	n/a	n/a
3	TCF12	chr5:98108409-98110611	A549	lung:	n/a	chr5:98110256-98110265
4	MAX	chr5:98108437-98110865	HepG2	liver:	n/a	chr5:98109181-98109191
5	MAZ	chr5:98108020-98110605	IMR90	lung:	n/a	chr5:98109181-98109191
6	MAX	chr5:98108320-98110731	HCT-116	colon:	n/a	chr5:98109181-98109191
7	SMARCC1	chr5:98109332-98110683	Hela-S3	cervix:	n/a	n/a
8	MAX	chr5:98108518-98110763	MCF-7	breast:	n/a	chr5:98109181-98109191
9	MYC	chr5:98109982-98110625	MCF10A-Er-Src	breast:	n/a	n/a
10	RFX5	chr5:98108655-98110586	Hela-S3	cervix:	n/a	chr5:98108834-98108843
11	MYC	chr5:98108670-98110578	MCF10A-Er-Src	breast:	n/a	chr5:98109181-98109191
12	TAF1	chr5:98110499-98110685	SK-N-SH	brain:	n/a	n/a
13	SIN3AK20	chr5:98110120-98110660	PFSK-1	brain:	n/a	n/a
14	MAX	chr5:98108627-98110737	GM12878	blood:	n/a	chr5:98109181-98109191
15	ELF1	chr5:98108548-98110605	GM12878	blood:	n/a	chr5:98109539-98109548 chr5:98109449-98109461 chr5:98109535-98109547
16	HCFC1	chr5:98108112-98110714	Hela-S3	cervix:	n/a	n/a
17	E2F6	chr5:98108284-98110633	A549	lung:	n/a	chr5:98109353-98109363 chr5:98108835-98108844 chr5:98109181-98109190 chr5:98109594-98109604 chr5:98109574-98109584
18	USF2	chr5:98110186-98110597	Hela-S3	cervix:	n/a	n/a
19	RCOR1	chr5:98108644-98110612	Hela-S3	cervix:	n/a	n/a
20	MYC	chr5:98108396-98110663	A549	lung:	n/a	chr5:98109181-98109191
21	KAP1	chr5:98110023-98110567	HEK293	kidney:	n/a	chr5:98110117-98110125
22	SIN3AK20	chr5:98110061-98110679	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr5:98108439-98110648	H1-hESC	embryonic stem cell:	n/a	n/a
24	MXI1	chr5:98108693-98110720	HepG2	liver:	n/a	n/a
25	MAX	chr5:98108499-98110731	H1-hESC	embryonic stem cell:	n/a	chr5:98109181-98109191
26	POLR2A	chr5:98103782-98112496	IMR90	lung:	n/a	n/a
27	POLR2A	chr5:98108561-98110631	Hela-S3	cervix:	n/a	n/a
28	CHD1	chr5:98110255-98110830	H1-hESC	embryonic stem cell:	n/a	chr5:98110353-98110363
29	MAX	chr5:98108489-98110699	ECC-1	luminal epithelium:	n/a	chr5:98109181-98109191
30	POLR2A	chr5:98108465-98110670	H1-neurons	neurons:	n/a	n/a
31	SIN3AK20	chr5:98108525-98110690	PANC-1	pancreas:	n/a	n/a
32	E2F6	chr5:98110018-98110543	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr5:98108523-98110700	Hela-S3	cervix:	n/a	n/a
34	ZNF263	chr5:98107892-98110575	HEK293-T-REx	kidney:	n/a	chr5:98109086-98109107 chr5:98109255-98109264
35	MAX	chr5:98109969-98110687	SK-N-SH	brain:	n/a	n/a
36	TCF7L2	chr5:98108491-98110608	Hela-S3	cervix:	n/a	n/a
37	E2F6	chr5:98110460-98110598	K562	blood:	n/a	n/a
38	MAX	chr5:98108535-98110654	Hela-S3	cervix:	n/a	chr5:98109181-98109191
39	KAP1	chr5:98110055-98110577	U2OS	brain:	n/a	chr5:98110117-98110125
40	CTBP2	chr5:98108860-98110651	H1-hESC	embryonic stem cell:	n/a	n/a
41	SIN3AK20	chr5:98109618-98110831	MCF-7	breast:	n/a	n/a
42	MAX	chr5:98108478-98110741	MCF-7	breast:	n/a	chr5:98109181-98109191
43	MAX	chr5:98108471-98110770	HepG2	liver:	n/a	chr5:98109181-98109191
44	MXI1	chr5:98107889-98112517	IMR90	lung:	n/a	n/a
45	SMARCB1	chr5:98108570-98110585	Hela-S3	cervix:	n/a	n/a
46	SIN3A	chr5:98108392-98111565	H1-hESC	embryonic stem cell:	n/a	chr5:98109597-98109608 chr5:98109985-98109998 chr5:98110167-98110180
47	REST	chr5:98108334-98110648	H1-neurons	neurons:	n/a	chr5:98109985-98109998
48	CHD1	chr5:98103004-98112580	IMR90	lung:	n/a	chr5:98110353-98110363 chr5:98104638-98104648
49	MAX	chr5:98108435-98110742	ECC-1	luminal epithelium:	n/a	chr5:98109181-98109191
50	HA-E2F1	chr5:98108345-98110719	MCF-7	breast:	n/a	chr5:98109353-98109363 chr5:98108835-98108844 chr5:98109181-98109190 chr5:98109594-98109604 chr5:98109574-98109584

No.	Distal block	Cell Line	Cell type
1	chr5:98103871..98107404-chr5:98108128..98112327,8	MCF-7	breast:
2	chr5:98102131..98106489-chr5:98107320..98111501,11	MCF-7	breast:
3	chr5:96517103..96519459-chr5:98107837..98111064,3	MCF-7	breast:

Variant related genes	Relation type
RGMB-AS1	TF binding region
ENSG00000058729	Chromatin interaction
ENSG00000174136	Chromatin interaction
ENSG00000251513	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10463992	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10900866	0.82[ASN][1000 genomes]
rs11242488	0.82[ASN][1000 genomes]
rs12513899	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12515608	0.89[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12518567	0.89[CEU][hapmap];0.84[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12521450	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17166353	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2080892	0.82[ASN][1000 genomes]
rs2302981	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2302983	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3952931	0.88[AMR][1000 genomes]
rs4018049	0.82[ASN][1000 genomes]
rs59968659	0.81[AMR][1000 genomes]
rs67111144	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs67755922	0.82[ASN][1000 genomes]
rs72773643	0.88[AMR][1000 genomes]
rs72773645	0.88[AMR][1000 genomes]
rs72773646	0.83[AMR][1000 genomes]
rs72773650	0.88[AMR][1000 genomes]
rs72773652	0.88[AMR][1000 genomes]
rs72773654	0.88[AMR][1000 genomes]
rs72773674	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72773675	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72773678	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7727348	0.86[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][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	nsv882414	chr5:98063710-98193164	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv3339628	chr5:98107452-98111750	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
3	esv3394593	chr5:98108277-98110825	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98103800-98112600	Active TSS	Rectal Smooth Muscle	rectum
2	chr5:98104000-98111400	Active TSS	Psoas Muscle	Psoas
3	chr5:98104000-98113400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:98104200-98111600	Active TSS	Right Atrium	heart
5	chr5:98104400-98110800	Active TSS	HSMMtube	muscle
6	chr5:98108200-98111000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr5:98108200-98111000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr5:98108200-98111000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr5:98108200-98112200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:98108200-98112400	Active TSS	Colonic Mucosa	Colon
11	chr5:98108400-98110600	Active TSS	HSMM	muscle
12	chr5:98108400-98110800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:98108400-98111000	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr5:98108400-98111000	Active TSS	Esophagus	oesophagus
15	chr5:98108400-98111200	Active TSS	H1 Cell Line	embryonic stem cell
16	chr5:98108400-98111200	Active TSS	H9 Cell Line	embryonic stem cell
17	chr5:98108400-98111200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:98108400-98111200	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr5:98108400-98111200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:98108400-98111200	Active TSS	Brain Angular Gyrus	brain
21	chr5:98108400-98111600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:98108400-98111600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:98108400-98111600	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr5:98108400-98111800	Active TSS	Pancreas	Pancrea
25	chr5:98108400-98112200	Active TSS	Ovary	ovary
26	chr5:98108400-98112400	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr5:98108600-98110600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
28	chr5:98108600-98110800	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr5:98108600-98110800	Active TSS	Brain Hippocampus Middle	brain
30	chr5:98108600-98110800	Active TSS	Small Intestine	intestine
31	chr5:98108600-98110800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
32	chr5:98108600-98111000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:98108600-98111000	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr5:98108600-98111200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:98108600-98111200	Active TSS	Brain Anterior Caudate	brain
36	chr5:98108600-98111200	Active TSS	Brain Cingulate Gyrus	brain
37	chr5:98108600-98111200	Active TSS	Fetal Kidney	kidney
38	chr5:98108600-98111200	Active TSS	Left Ventricle	heart
39	chr5:98108600-98111600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:98108800-98110600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:98108800-98110600	Active TSS	Fetal Intestine Large	intestine
42	chr5:98108800-98110600	Active TSS	Fetal Lung	lung
43	chr5:98108800-98110600	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr5:98108800-98110600	Active TSS	Spleen	Spleen
45	chr5:98108800-98110800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:98108800-98110800	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr5:98108800-98110800	Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr5:98108800-98110800	Active TSS	Aorta	Aorta
49	chr5:98108800-98110800	Active TSS	Brain Substantia Nigra	brain
50	chr5:98108800-98110800	Active TSS	Duodenum Mucosa	Duodenum

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