Variant report

Variant	rs6716999
Chromosome Location	chr2:11886415-11886416
allele	A/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	MAX	chr2:11884708-11887762	HepG2	liver:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
2	ELF1	chr2:11886103-11887523	GM12878	blood:	n/a	chr2:11886833-11886845 chr2:11886742-11886751
3	SP1	chr2:11886415-11886919	GM12878	blood:	n/a	chr2:11886561-11886570 chr2:11886561-11886571 chr2:11886561-11886571 chr2:11886560-11886572 chr2:11886560-11886572 chr2:11886562-11886571
4	MAX	chr2:11886355-11887595	K562	blood:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
5	EP300	chr2:11886332-11887720	SK-N-SH	brain:	n/a	chr2:11887150-11887166 chr2:11886742-11886751
6	MXI1	chr2:11886239-11888165	IMR90	lung:	n/a	n/a
7	TCF7L2	chr2:11885779-11887411	HEK293	kidney:	n/a	n/a
8	JUN	chr2:11886348-11886886	K562	blood:	n/a	n/a
9	WRNIP1	chr2:11886333-11886527	GM12878	blood:	n/a	n/a
10	BCL3	chr2:11886333-11886874	A549	lung:	n/a	chr2:11886745-11886758 chr2:11886834-11886847
11	HDAC2	chr2:11886365-11887494	HepG2	liver:	n/a	chr2:11886423-11886431 chr2:11886529-11886543 chr2:11887222-11887236
12	MXI1	chr2:11886378-11887515	HepG2	liver:	n/a	n/a
13	SIN3A	chr2:11886214-11887595	H1-hESC	embryonic stem cell:	n/a	chr2:11887129-11887143
14	MXI1	chr2:11885917-11888799	SK-N-SH	brain:	n/a	n/a
15	TCF12	chr2:11886167-11887768	A549	lung:	n/a	chr2:11886616-11886626
16	CTCF	chr2:11886340-11886490	GM12874	blood:	n/a	n/a
17	RCOR1	chr2:11886370-11887273	HepG2	liver:	n/a	n/a
18	CTCF	chr2:11886280-11886430	A549	lung:	n/a	n/a
19	PBX3	chr2:11886356-11887062	SK-N-SH	brain:	n/a	n/a
20	SP1	chr2:11886271-11887022	A549	lung:	n/a	chr2:11886982-11886991 chr2:11886561-11886570 chr2:11886561-11886571 chr2:11886561-11886571 chr2:11886983-11886992 chr2:11886978-11886992 chr2:11886560-11886572 chr2:11886560-11886572 chr2:11886562-11886571
21	E2F6	chr2:11886153-11887313	K562	blood:	n/a	chr2:11886745-11886754 chr2:11886982-11886994 chr2:11886743-11886753 chr2:11886982-11886991 chr2:11886295-11886302
22	FOSL2	chr2:11886328-11886985	SK-N-SH	brain:	n/a	n/a
23	FOSL2	chr2:11886338-11886826	A549	lung:	n/a	n/a
24	RCOR1	chr2:11885844-11887559	K562	blood:	n/a	n/a
25	CBX3	chr2:11886347-11886918	K562	blood:	n/a	n/a
26	MYBL2	chr2:11886273-11886906	HepG2	liver:	n/a	n/a
27	RCOR1	chr2:11886393-11887083	K562	blood:	n/a	n/a
28	HMGN3	chr2:11886184-11887329	K562	blood:	n/a	n/a
29	SIN3AK20	chr2:11886326-11887677	MCF-7	breast:	n/a	n/a
30	MAX	chr2:11886351-11887566	HCT-116	colon:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
31	SMARCB1	chr2:11886246-11887468	Hela-S3	cervix:	n/a	n/a
32	MAZ	chr2:11886410-11887586	GM12878	blood:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
33	POLR2A	chr2:11886374-11886670	HCT-116	colon:	n/a	n/a
34	EP300	chr2:11886341-11886918	K562	blood:	n/a	chr2:11886742-11886751
35	TCF12	chr2:11886387-11887275	ECC-1	luminal epithelium:	n/a	chr2:11886616-11886626
36	TEAD4	chr2:11886388-11886692	K562	blood:	n/a	n/a
37	MAZ	chr2:11885735-11887744	IMR90	lung:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
38	ZEB1	chr2:11886255-11886540	GM12878	blood:	n/a	n/a
39	MAZ	chr2:11886381-11887366	HepG2	liver:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
40	MAX	chr2:11886369-11887565	A549	lung:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
41	EP300	chr2:11886292-11887719	ECC-1	luminal epithelium:	n/a	chr2:11887150-11887166 chr2:11886742-11886751
42	MAX	chr2:11886392-11887116	H1-hESC	embryonic stem cell:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
43	MYC	chr2:11886385-11887897	K562	blood:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
44	MAX	chr2:11886056-11887651	HepG2	liver:	n/a	chr2:11886898-11886908 chr2:11886778-11886787
45	NR2F2	chr2:11886348-11887653	MCF-7	breast:	n/a	n/a
46	HEY1	chr2:11886367-11887075	HepG2	liver:	n/a	n/a
47	JUND	chr2:11886389-11886956	K562	blood:	n/a	n/a
48	POLR2A	chr2:11886352-11887081	U87	brain:	n/a	n/a
49	SIN3AK20	chr2:11886411-11887319	PANC-1	pancreas:	n/a	n/a
50	MAX	chr2:11886320-11887666	A549	lung:	n/a	chr2:11886898-11886908 chr2:11886778-11886787

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:11886400-11886450	ovcar-3	ovarian:	n/a
2	chr2:11886400-11886450	LNCaP	prostate:	n/a
3	chr2:11886400-11886450	GM12891	blood:	n/a
4	chr2:11886400-11886450	AG04450	lung:	fetal
5	chr2:11886400-11886450	HAEpiC	amniotic membrane:	n/a
6	chr2:11886400-11886450	HUVEC	blood vessel:	n/a
7	chr2:11886400-11886450	HCPEpiC	choroid plexus:	n/a
8	chr2:11886400-11886450	AoSMC	blood vessel:	n/a
9	chr2:11886400-11886450	Hepatocyte	liver:	n/a
10	chr2:11886400-11886450	GM12878	blood:	n/a
11	chr2:11886400-11886450	GM19239	blood:	n/a
12	chr2:11886400-11886450	BJ	skin:	n/a
13	chr2:11886400-11886450	K562	blood:	n/a
14	chr2:11886400-11886450	SKMC	muscle:	n/a
15	chr2:11886400-11886450	HEK293	kidney:	embryo
16	chr2:11886400-11886450	HIPEpiC	eye:	n/a
17	chr2:11886400-11886450	HL-60	blood:	n/a
18	chr2:11886400-11886450	NHDF-neo	bronchial:	n/a
19	chr2:11886400-11886450	AG09319	gingival:	n/a
20	chr2:11886400-11886450	Caco-2	colon:	n/a
21	chr2:11886400-11886450	NH-A	brain:	n/a
22	chr2:11886400-11886450	NHBE	bronchial:	n/a
23	chr2:11886400-11886450	HepG2	liver:	n/a
24	chr2:11886400-11886450	HEEpiC	esophagus:	n/a
25	chr2:11886400-11886450	AG09309	skin:	n/a
26	chr2:11886400-11886450	GM06990	blood:	n/a
27	chr2:11886400-11886450	PFSK-1	brain:	n/a
28	chr2:11886400-11886450	HMEC	breast:	n/a
29	chr2:11886400-11886450	HCF	heart:	n/a
30	chr2:11886400-11886450	AG10803	skin:	n/a
31	chr2:11886400-11886450	A549	lung:	n/a
32	chr2:11886400-11886450	AG04449	skin:	fetal
33	chr2:11886400-11886450	HNPCEpiC	eye:	n/a
34	chr2:11886400-11886450	MCF-7	breast:	n/a
35	chr2:11886400-11886450	HRE	kidney:	n/a
36	chr2:11886400-11886450	BE2_C	brain:	n/a
37	chr2:11886400-11886450	U87	brain:	n/a
38	chr2:11886400-11886450	NT2-D1	testis:	n/a
39	chr2:11886400-11886450	IMR90	lung:	fetal
40	chr2:11886400-11886450	SK-N-SH	brain:	n/a
41	chr2:11886400-11886450	HRCEpiC	kidney:	n/a
42	chr2:11886400-11886450	Jurkat	blood:	n/a
43	chr2:11886400-11886450	HRPEpiC	eye:	n/a
44	chr2:11886400-11886450	HCT-116	colon:	n/a
45	chr2:11886400-11886450	NB4	blood:	n/a
46	chr2:11886400-11886450	ProgFib	skin:	n/a
47	chr2:11886400-11886450	GM12892	blood:	n/a
48	chr2:11886400-11886450	SAEC	small airway:	n/a
49	chr2:11886400-11886450	MCF10A-Er-Src	breast:	n/a
50	chr2:11886400-11886450	HPAEpiC	pulmonary alveolar:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11604255..11606398-chr2:11886112..11888104,2	K562	blood:
2	chr2:11881178..11885762-chr2:11886043..11889477,7	MCF-7	breast:
3	chr2:11885343..11888558-chr2:11916972..11921085,4	K562	blood:
4	chr2:11678361..11681033-chr2:11884649..11887386,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230790	TF binding region
LPIN1	TF binding region
ENSG00000230790	CpG island
LPIN1	CpG island
ENSG00000134324	Chromatin interaction
ENSG00000230790	Chromatin interaction
ENSG00000264010	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000169016	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1036393	1.00[ASN][1000 genomes]
rs11538448	1.00[ASN][1000 genomes]
rs11675463	1.00[ASN][1000 genomes]
rs11676175	1.00[ASN][1000 genomes]
rs11677240	1.00[ASN][1000 genomes]
rs11683719	1.00[ASN][1000 genomes]
rs11890442	1.00[ASN][1000 genomes]
rs11892871	1.00[ASN][1000 genomes]
rs11894146	1.00[ASN][1000 genomes]
rs11894751	1.00[ASN][1000 genomes]
rs13421972	1.00[ASN][1000 genomes]
rs1561010	1.00[ASN][1000 genomes]
rs1561011	1.00[ASN][1000 genomes]
rs16857679	1.00[ASN][1000 genomes]
rs34592059	1.00[ASN][1000 genomes]
rs34928762	1.00[ASN][1000 genomes]
rs45509591	1.00[ASN][1000 genomes]
rs55890755	1.00[ASN][1000 genomes]
rs56788115	1.00[ASN][1000 genomes]
rs57097271	1.00[ASN][1000 genomes]
rs59085046	1.00[ASN][1000 genomes]
rs59208217	1.00[ASN][1000 genomes]
rs59408163	1.00[ASN][1000 genomes]
rs60662456	1.00[ASN][1000 genomes]
rs61239977	1.00[ASN][1000 genomes]
rs62113260	1.00[ASN][1000 genomes]
rs62113263	1.00[ASN][1000 genomes]
rs62113264	1.00[ASN][1000 genomes]
rs62113265	1.00[ASN][1000 genomes]
rs62113266	1.00[ASN][1000 genomes]
rs62113267	1.00[ASN][1000 genomes]
rs62113293	1.00[ASN][1000 genomes]
rs62113296	1.00[ASN][1000 genomes]
rs62113297	1.00[ASN][1000 genomes]
rs62113298	1.00[ASN][1000 genomes]
rs62113299	1.00[ASN][1000 genomes]
rs62113300	1.00[ASN][1000 genomes]
rs62113302	1.00[ASN][1000 genomes]
rs62113303	1.00[ASN][1000 genomes]
rs62113305	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113307	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62113308	1.00[ASN][1000 genomes]
rs62113309	1.00[ASN][1000 genomes]
rs62113310	1.00[ASN][1000 genomes]
rs62113313	1.00[ASN][1000 genomes]
rs62113354	1.00[ASN][1000 genomes]
rs62113357	1.00[ASN][1000 genomes]
rs62114961	1.00[ASN][1000 genomes]
rs62114962	1.00[ASN][1000 genomes]
rs62114963	1.00[ASN][1000 genomes]
rs62114964	1.00[ASN][1000 genomes]
rs62114967	1.00[ASN][1000 genomes]
rs62114968	1.00[ASN][1000 genomes]
rs62116185	1.00[ASN][1000 genomes]
rs62116208	1.00[ASN][1000 genomes]
rs62116209	1.00[ASN][1000 genomes]
rs6707885	1.00[ASN][1000 genomes]
rs6717771	1.00[ASN][1000 genomes]
rs6726960	1.00[ASN][1000 genomes]
rs6744695	1.00[ASN][1000 genomes]
rs6744803	1.00[ASN][1000 genomes]
rs71446421	1.00[ASN][1000 genomes]
rs72773987	1.00[ASN][1000 genomes]
rs72773997	1.00[ASN][1000 genomes]
rs72773999	1.00[ASN][1000 genomes]
rs72774000	1.00[ASN][1000 genomes]
rs7566112	1.00[ASN][1000 genomes]
rs7566488	1.00[ASN][1000 genomes]
rs7569901	1.00[ASN][1000 genomes]
rs7570139	1.00[ASN][1000 genomes]
rs7575000	1.00[ASN][1000 genomes]
rs7593837	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv580973	chr2:11864946-11898931	Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv580974	chr2:11867841-11898931	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11882600-11886800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:11882800-11886600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:11883400-11887000	Enhancers	Placenta	Placenta
4	chr2:11883600-11886800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:11883800-11886800	Enhancers	Lung	lung
6	chr2:11883800-11886800	Enhancers	Spleen	Spleen
7	chr2:11884400-11886600	Enhancers	Small Intestine	intestine
8	chr2:11884600-11886800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:11885000-11886600	Enhancers	Gastric	stomach
10	chr2:11885200-11886800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:11886000-11886600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:11886000-11886600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:11886000-11886600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:11886000-11886600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:11886000-11886600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:11886000-11886600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:11886000-11886600	Flanking Active TSS	Brain Angular Gyrus	brain
18	chr2:11886000-11886600	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr2:11886000-11886600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:11886000-11886600	Flanking Active TSS	Esophagus	oesophagus
21	chr2:11886000-11886600	Enhancers	Fetal Brain Male	brain
22	chr2:11886000-11886600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr2:11886000-11886600	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr2:11886000-11886600	Flanking Active TSS	Dnd41	blood
25	chr2:11886000-11886600	Flanking Active TSS	GM12878-XiMat	blood
26	chr2:11886000-11886600	Flanking Active TSS	Hela-S3	cervix
27	chr2:11886000-11886600	Flanking Active TSS	K562	blood
28	chr2:11886000-11886600	Flanking Active TSS	NHEK	skin
29	chr2:11886000-11886800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:11886000-11887400	Active TSS	H9 Cell Line	embryonic stem cell
31	chr2:11886000-11887400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr2:11886000-11888000	Active TSS	Brain Germinal Matrix	brain
33	chr2:11886200-11886600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:11886200-11886600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr2:11886200-11886600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr2:11886200-11886600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr2:11886200-11886600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:11886200-11886600	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr2:11886200-11886600	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr2:11886200-11886600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr2:11886200-11886600	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr2:11886200-11886600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr2:11886200-11886600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr2:11886200-11886600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr2:11886200-11886600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:11886200-11886600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr2:11886200-11886600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr2:11886200-11886600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:11886200-11886600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:11886200-11886600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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