Variant report

Variant	rs11685543
Chromosome Location	chr2:11606647-11606648
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	POLR2A	chr2:11605868-11606969	Raji	blood:	n/a	n/a
2	EP300	chr2:11606235-11606828	K562	blood:	n/a	n/a
3	RFX5	chr2:11605223-11608297	SK-N-SH	brain:	n/a	n/a
4	ZNF384	chr2:11606310-11606671	GM12878	blood:	n/a	n/a
5	GABPA	chr2:11606155-11606896	MCF-7	breast:	n/a	chr2:11606297-11606311 chr2:11606297-11606308 chr2:11606294-11606308
6	MTA3	chr2:11606196-11606947	GM12878	blood:	n/a	n/a
7	TEAD4	chr2:11606093-11606815	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:11605487-11606671	SK-N-SH	brain:	n/a	n/a
9	MAX	chr2:11605348-11607155	HepG2	liver:	n/a	chr2:11605840-11605850
10	SP1	chr2:11605481-11606947	A549	lung:	n/a	chr2:11606408-11606419 chr2:11605835-11605849
11	POLR2A	chr2:11605450-11606718	PFSK-1	brain:	n/a	n/a
12	SP1	chr2:11606091-11606676	HepG2	liver:	n/a	chr2:11606408-11606419
13	MAX	chr2:11605423-11606676	ECC-1	luminal epithelium:	n/a	chr2:11605840-11605850
14	TAF1	chr2:11605879-11606655	ECC-1	luminal epithelium:	n/a	n/a
15	ZBTB33	chr2:11606229-11606664	SK-N-SH	brain:	n/a	n/a
16	STAT5A	chr2:11605829-11606654	K562	blood:	n/a	chr2:11605865-11605877
17	REST	chr2:11605476-11606648	A549	lung:	n/a	chr2:11606338-11606351
18	TEAD4	chr2:11606128-11606673	A549	lung:	n/a	n/a
19	TEAD4	chr2:11605314-11606685	K562	blood:	n/a	n/a
20	RCOR1	chr2:11606205-11606798	Hela-S3	cervix:	n/a	n/a
21	TCF12	chr2:11605213-11607109	A549	lung:	n/a	chr2:11606482-11606490
22	SP1	chr2:11605365-11607057	A549	lung:	n/a	chr2:11606408-11606419 chr2:11605835-11605849
23	MAX	chr2:11605539-11606906	Hela-S3	cervix:	n/a	chr2:11605840-11605850
24	SIN3AK20	chr2:11605596-11606891	PANC-1	pancreas:	n/a	n/a
25	JUND	chr2:11606236-11606690	T-47D	breast:	n/a	chr2:11606362-11606376
26	POLR2A	chr2:11605378-11606784	U87	brain:	n/a	n/a
27	GATA3	chr2:11605251-11606779	A549	lung:	n/a	chr2:11605426-11605436
28	CREB1	chr2:11605585-11606857	A549	lung:	n/a	n/a
29	TAF1	chr2:11605610-11606704	A549	lung:	n/a	n/a
30	POLR2A	chr2:11605517-11606919	GM12891	blood:	n/a	n/a
31	POLR2A	chr2:11605618-11606668	HUVEC	blood vessel:	n/a	n/a
32	NR2F2	chr2:11605593-11607054	K562	blood:	n/a	n/a
33	MAX	chr2:11605305-11606929	MCF-7	breast:	n/a	chr2:11605840-11605850
34	JUN	chr2:11605303-11607477	K562	blood:	n/a	chr2:11606362-11606376 chr2:11605517-11605531
35	SIX5	chr2:11605992-11606763	A549	lung:	n/a	n/a
36	MYBL2	chr2:11605281-11607072	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:11605594-11606654	K562	blood:	n/a	n/a
38	YY1	chr2:11605577-11606711	HepG2	liver:	n/a	chr2:11606255-11606275 chr2:11605826-11605835 chr2:11605829-11605838 chr2:11606257-11606269
39	REST	chr2:11605926-11606915	H1-neurons	neurons:	n/a	chr2:11606338-11606351
40	MAX	chr2:11605530-11606805	Hela-S3	cervix:	n/a	chr2:11605840-11605850
41	MYC	chr2:11605418-11606648	K562	blood:	n/a	chr2:11605840-11605850
42	POLR2A	chr2:11605588-11607070	K562	blood:	n/a	n/a
43	SIN3AK20	chr2:11605290-11606754	MCF-7	breast:	n/a	n/a
44	EP300	chr2:11605471-11606653	A549	lung:	n/a	n/a
45	MAX	chr2:11605285-11607149	A549	lung:	n/a	chr2:11605840-11605850
46	ATF3	chr2:11606118-11606652	A549	lung:	n/a	n/a
47	POLR2A	chr2:11605425-11607084	HUVEC	blood vessel:	n/a	n/a
48	SP1	chr2:11606102-11606687	H1-hESC	embryonic stem cell:	n/a	chr2:11606408-11606419
49	ATF3	chr2:11606100-11606665	A549	lung:	n/a	n/a
50	EGR1	chr2:11606102-11606816	HCT-116	colon:	n/a	chr2:11606316-11606338

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11292916..11295580-chr2:11604494..11607840,3	MCF-7	breast:
2	chr2:11604833..11608003-chr2:11882353..11886330,4	K562	blood:

Variant related genes	Relation type
E2F6	TF binding region
ENSG00000162976	Chromatin interaction
ENSG00000230790	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10186511	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10192676	0.85[ASN][1000 genomes]
rs10803737	0.84[ASN][1000 genomes]
rs10929740	0.83[ASN][1000 genomes]
rs10929741	0.81[ASN][1000 genomes]
rs10929742	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10929745	0.86[ASN][1000 genomes]
rs10929746	0.86[ASN][1000 genomes]
rs10929747	0.86[ASN][1000 genomes]
rs10929748	0.86[ASN][1000 genomes]
rs10929749	0.86[ASN][1000 genomes]
rs11680919	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11686138	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11687178	0.89[ASN][1000 genomes]
rs11687681	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11693023	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11694857	0.89[ASN][1000 genomes]
rs12472962	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12611958	0.89[ASN][1000 genomes]
rs12615317	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12988106	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1369500	0.86[ASN][1000 genomes]
rs1369501	0.86[ASN][1000 genomes]
rs1369502	0.86[ASN][1000 genomes]
rs1369503	0.86[ASN][1000 genomes]
rs34075853	0.86[ASN][1000 genomes]
rs35047869	0.86[ASN][1000 genomes]
rs35160324	0.86[ASN][1000 genomes]
rs35306821	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35606161	0.86[ASN][1000 genomes]
rs35727311	0.89[ASN][1000 genomes]
rs35734540	0.86[ASN][1000 genomes]
rs35818376	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35973068	0.86[ASN][1000 genomes]
rs4292073	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4491705	0.80[ASN][1000 genomes]
rs4553788	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4668726	0.88[EUR][1000 genomes]
rs60323348	0.86[ASN][1000 genomes]
rs60819231	0.86[ASN][1000 genomes]
rs61016299	0.89[ASN][1000 genomes]
rs6432193	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6432195	0.80[ASN][1000 genomes]
rs6432196	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6432197	0.86[ASN][1000 genomes]
rs6432198	0.86[ASN][1000 genomes]
rs6432200	0.84[EUR][1000 genomes]
rs6705284	0.86[ASN][1000 genomes]
rs6714698	0.86[ASN][1000 genomes]
rs6719876	0.86[ASN][1000 genomes]
rs6724082	0.86[ASN][1000 genomes]
rs6724463	0.86[ASN][1000 genomes]
rs6729114	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6751915	0.89[ASN][1000 genomes]
rs6753836	0.86[ASN][1000 genomes]
rs7425786	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7556984	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7565965	0.86[ASN][1000 genomes]
rs7577942	0.86[ASN][1000 genomes]
rs7584175	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9789694	0.82[EUR][1000 genomes];0.89[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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11604400-11607000	Active TSS	Ovary	ovary
2	chr2:11604400-11607000	Active TSS	Psoas Muscle	Psoas
3	chr2:11604600-11606800	Active TSS	Brain Angular Gyrus	brain
4	chr2:11604600-11607200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:11604800-11606800	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr2:11604800-11606800	Active TSS	Right Ventricle	heart
7	chr2:11604800-11607200	Active TSS	Stomach Smooth Muscle	stomach
8	chr2:11605000-11606800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:11605000-11606800	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr2:11605000-11606800	Active TSS	Muscle Satellite Cultured Cells	--
11	chr2:11605000-11606800	Active TSS	Right Atrium	heart
12	chr2:11605000-11607000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:11605000-11607000	Active TSS	Brain Anterior Caudate	brain
14	chr2:11605000-11607000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr2:11605000-11607200	Active TSS	Rectal Smooth Muscle	rectum
16	chr2:11605200-11606800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:11605200-11606800	Active TSS	HSMMtube	muscle
18	chr2:11605200-11607000	Active TSS	A549	lung
19	chr2:11605200-11607000	Active TSS	NHLF	lung
20	chr2:11605400-11606800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr2:11605400-11606800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr2:11605400-11606800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
23	chr2:11605400-11606800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
24	chr2:11605400-11606800	Active TSS	Esophagus	oesophagus
25	chr2:11605400-11606800	Active TSS	Gastric	stomach
26	chr2:11605400-11606800	Active TSS	Left Ventricle	heart
27	chr2:11605400-11606800	Active TSS	Pancreas	Pancrea
28	chr2:11605400-11606800	Active TSS	Sigmoid Colon	Sigmoid Colon
29	chr2:11605400-11607000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:11605400-11607000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:11605400-11607000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr2:11605400-11607400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:11605600-11606800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:11605600-11606800	Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr2:11605600-11606800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:11605600-11606800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr2:11605600-11606800	Active TSS	Aorta	Aorta
38	chr2:11605600-11606800	Active TSS	Brain Germinal Matrix	brain
39	chr2:11605600-11606800	Active TSS	Brain Hippocampus Middle	brain
40	chr2:11605600-11606800	Active TSS	Colon Smooth Muscle	Colon
41	chr2:11605600-11606800	Active TSS	Small Intestine	intestine
42	chr2:11605600-11606800	Active TSS	Spleen	Spleen
43	chr2:11605600-11607000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr2:11605600-11607000	Active TSS	Brain Substantia Nigra	brain
45	chr2:11605600-11607000	Active TSS	Fetal Intestine Large	intestine
46	chr2:11605600-11607000	Active TSS	Fetal Kidney	kidney
47	chr2:11605600-11607000	Active TSS	Fetal Lung	lung
48	chr2:11605600-11607000	Active TSS	Stomach Mucosa	stomach
49	chr2:11605600-11607000	Active TSS	HSMM	muscle
50	chr2:11605600-11607000	Active TSS	NHDF-Ad	bronchial

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