Variant report

Variant	rs7559835
Chromosome Location	chr2:11723311-11723312
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	JUND	chr2:11722962-11723344	HepG2	liver:	n/a	chr2:11723150-11723162 chr2:11723152-11723161 chr2:11723153-11723160 chr2:11723150-11723161 chr2:11723151-11723161 chr2:11723152-11723160 chr2:11723245-11723254
2	CTCF	chr2:11721671-11723784	SK-N-SH	brain:	n/a	chr2:11723015-11723028 chr2:11723019-11723028 chr2:11723013-11723031 chr2:11723018-11723031
3	MYBL2	chr2:11722722-11723839	HepG2	liver:	n/a	n/a
4	RFX5	chr2:11722946-11723712	HepG2	liver:	n/a	n/a
5	ELF1	chr2:11723311-11723661	HepG2	liver:	n/a	n/a
6	CTCF	chr2:11723280-11723430	WERI-Rb-1	eye:	n/a	n/a
7	FOXA1	chr2:11722788-11723906	HepG2	liver:	n/a	chr2:11723592-11723604
8	POLR2A	chr2:11720876-11723810	HepG2	liver:	n/a	n/a
9	JUN	chr2:11723029-11723349	HepG2	liver:	n/a	chr2:11723150-11723162 chr2:11723152-11723161 chr2:11723153-11723160 chr2:11723151-11723161 chr2:11723152-11723160 chr2:11723245-11723254
10	MXI1	chr2:11722854-11723662	HepG2	liver:	n/a	n/a
11	MAZ	chr2:11723022-11723396	HepG2	liver:	n/a	chr2:11723151-11723160 chr2:11723152-11723161
12	MAX	chr2:11722502-11723331	A549	lung:	n/a	chr2:11722952-11722962 chr2:11723151-11723160 chr2:11723152-11723161
13	SMC3	chr2:11722824-11723543	HepG2	liver:	n/a	chr2:11723015-11723029 chr2:11723015-11723025 chr2:11722825-11722839 chr2:11723021-11723031
14	FOXA2	chr2:11723294-11723806	A549	lung:	n/a	chr2:11723592-11723604
15	POLR2A	chr2:11712005-11732311	MCF-7	breast:	n/a	n/a
16	CTCF	chr2:11722732-11723332	HCT-116	colon:	n/a	chr2:11723015-11723028 chr2:11723019-11723028 chr2:11723013-11723031 chr2:11723018-11723031
17	JUND	chr2:11722824-11723446	H1-hESC	embryonic stem cell:	n/a	chr2:11723150-11723162 chr2:11723152-11723161 chr2:11723153-11723160 chr2:11723150-11723161 chr2:11723151-11723161 chr2:11723152-11723160 chr2:11723245-11723254
18	MYBL2	chr2:11722736-11723648	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:11721389-11723390	HepG2	liver:	n/a	n/a
20	PML	chr2:11722796-11723526	MCF-7	breast:	n/a	chr2:11723150-11723159 chr2:11723153-11723162
21	FOXA2	chr2:11722942-11724253	HepG2	liver:	n/a	chr2:11723592-11723604
22	EP300	chr2:11723240-11723750	HepG2	liver:	n/a	chr2:11723585-11723599 chr2:11723595-11723605 chr2:11723637-11723647
23	CTCF	chr2:11723260-11723410	GM12864	blood:	n/a	n/a
24	FOXA1	chr2:11723150-11723820	HepG2	liver:	n/a	chr2:11723592-11723604
25	RFX5	chr2:11722758-11723828	IMR90	lung:	n/a	n/a
26	CTCF	chr2:11723280-11723430	AoAF	blood vessel:	n/a	n/a
27	CTCF	chr2:11723297-11723383	Spleen_OC	spleen:	n/a	n/a
28	POLR2A	chr2:11722192-11723577	HepG2	liver:	n/a	n/a
29	RAD21	chr2:11722557-11723437	HCT-116	colon:	n/a	chr2:11723021-11723031 chr2:11722764-11722776 chr2:11723014-11723027 chr2:11723013-11723025 chr2:11723011-11723030 chr2:11723015-11723025 chr2:11722806-11722820
30	MBD4	chr2:11722764-11723753	HepG2	liver:	n/a	n/a
31	SIN3AK20	chr2:11721955-11724935	MCF-7	breast:	n/a	n/a
32	CTCF	chr2:11722464-11723781	A549	lung:	n/a	chr2:11723015-11723028 chr2:11723019-11723028 chr2:11723013-11723031 chr2:11723018-11723031
33	CTCF	chr2:11722689-11723326	K562	blood:	n/a	chr2:11723015-11723028 chr2:11723019-11723028 chr2:11723013-11723031 chr2:11723018-11723031
34	CTCF	chr2:11723309-11723390	GM20000	blood:	n/a	n/a
35	NR3C1	chr2:11722883-11723327	A549	lung:	n/a	chr2:11723027-11723053 chr2:11723027-11723053 chr2:11723027-11723053 chr2:11723027-11723053
36	SMC3	chr2:11722459-11723463	SK-N-SH	brain:	n/a	chr2:11723015-11723029 chr2:11723015-11723025 chr2:11722825-11722839 chr2:11723021-11723031
37	ZBTB7A	chr2:11723198-11723552	HepG2	liver:	n/a	n/a
38	MBD4	chr2:11722678-11723789	HepG2	liver:	n/a	n/a
39	EP300	chr2:11723297-11723787	HepG2	liver:	n/a	chr2:11723585-11723599 chr2:11723595-11723605 chr2:11723637-11723647
40	TEAD4	chr2:11722733-11723764	HepG2	liver:	n/a	n/a
41	FOXP2	chr2:11723281-11723698	SK-N-MC	brain:	n/a	chr2:11723592-11723604
42	RCOR1	chr2:11722925-11723550	HepG2	liver:	n/a	n/a
43	CTCF	chr2:11723280-11723430	NHEK	skin:	n/a	n/a
44	RAD21	chr2:11722551-11723549	SK-N-SH	brain:	n/a	chr2:11723021-11723031 chr2:11722764-11722776 chr2:11723014-11723027 chr2:11723013-11723025 chr2:11723011-11723030 chr2:11723015-11723025 chr2:11722806-11722820
45	POLR2A	chr2:11721551-11723534	HepG2	liver:	n/a	n/a
46	NFIC	chr2:11723224-11723818	HepG2	liver:	n/a	n/a
47	FOXA2	chr2:11723300-11723780	HepG2	liver:	n/a	chr2:11723592-11723604
48	CTCF	chr2:11722553-11723348	HCT-116	colon:	n/a	chr2:11723015-11723028 chr2:11723019-11723028 chr2:11723013-11723031 chr2:11723018-11723031
49	CTCF	chr2:11723281-11723350	GM12878	blood:	n/a	n/a
50	NFIC	chr2:11722870-11723644	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11674992..11675535-chr2:11722581..11723483,3	MCF-7	breast:
2	chr2:11617839..11618544-chr2:11722552..11723470,3	MCF-7	breast:
3	chr2:11723075..11724603-chr2:11731951..11734172,2	MCF-7	breast:
4	chr2:11617909..11619476-chr2:11722476..11723331,8	K562	blood:
5	chr2:11713329..11715208-chr2:11722167..11724043,2	K562	blood:
6	chr2:11272792..11273388-chr2:11722468..11723500,6	K562	blood:
7	chr2:11617635..11618699-chr2:11722537..11723549,3	MCF-7	breast:
8	chr2:11620284..11621192-chr2:11722895..11723465,2	K562	blood:

Variant related genes	Relation type
RN7SL674P	TF binding region
ENSG00000150873	Chromatin interaction
ENSG00000145063	Chromatin interaction

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

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

rs_ID	r²[population]
rs11681838	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11688915	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11689869	0.85[ASN][1000 genomes]
rs13004648	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs13009660	0.94[EUR][1000 genomes]
rs13431704	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13432243	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1435547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1865575	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs34507933	0.94[EUR][1000 genomes]
rs35023351	0.94[EUR][1000 genomes]
rs35188552	0.92[EUR][1000 genomes]
rs35217326	0.86[EUR][1000 genomes]
rs35587928	0.94[EUR][1000 genomes]
rs36030386	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669756	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs62118318	0.85[ASN][1000 genomes]
rs6724078	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs6736604	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6743256	0.94[EUR][1000 genomes]
rs6744817	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7557063	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7576944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596162	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs880858	1.00[ASN][1000 genomes]
rs9287733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11694800-11755200	Weak transcription	Gastric	stomach
3	chr2:11700000-11767000	Weak transcription	Right Atrium	heart
4	chr2:11709800-11724200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:11711600-11738600	Weak transcription	Left Ventricle	heart
6	chr2:11714400-11765000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:11717600-11767000	Weak transcription	Fetal Intestine Small	intestine
8	chr2:11719200-11725800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:11719200-11738000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:11719400-11750800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:11720000-11735600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:11721600-11733000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:11721800-11726000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:11722000-11724600	Enhancers	Fetal Muscle Leg	muscle
15	chr2:11722000-11725600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:11722200-11723400	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr2:11722200-11724600	Enhancers	Fetal Muscle Trunk	muscle
18	chr2:11722400-11723400	Enhancers	Fetal Lung	lung
19	chr2:11722400-11724400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:11722400-11724400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:11722600-11723600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr2:11722600-11723600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:11722600-11723600	Enhancers	Brain Hippocampus Middle	brain
24	chr2:11722600-11724200	Enhancers	Pancreas	Pancrea
25	chr2:11722600-11724400	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr2:11722600-11724800	Enhancers	Stomach Smooth Muscle	stomach
27	chr2:11722600-11724800	Enhancers	HSMMtube	muscle
28	chr2:11722800-11723400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr2:11722800-11723400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr2:11722800-11723800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:11722800-11724200	Enhancers	Placenta	Placenta
32	chr2:11722800-11724200	Enhancers	Ovary	ovary
33	chr2:11722800-11724400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:11722800-11724400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:11722800-11724400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:11722800-11724400	Enhancers	Fetal Stomach	stomach
37	chr2:11722800-11724400	Enhancers	HSMM	muscle
38	chr2:11722800-11724800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:11722800-11724800	Enhancers	Stomach Mucosa	stomach
40	chr2:11722800-11724800	Enhancers	NHDF-Ad	bronchial
41	chr2:11723000-11723600	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr2:11723000-11723600	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr2:11723000-11723600	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr2:11723000-11723800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr2:11723000-11723800	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr2:11723000-11723800	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr2:11723000-11724000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:11723000-11724200	Enhancers	Colon Smooth Muscle	Colon
49	chr2:11723000-11724400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:11723000-11724400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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