Variant report

Variant	rs4668301
Chromosome Location	chr2:171569066-171569067
allele	C/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	MYBL2	chr2:171567448-171569634	HepG2	liver:	n/a	n/a
2	TCF7L2	chr2:171568484-171569419	HepG2	liver:	n/a	chr2:171568813-171568822 chr2:171568705-171568714 chr2:171568951-171568960 chr2:171568809-171568825
3	NFIC	chr2:171567573-171570136	HepG2	liver:	n/a	n/a
4	ARID3A	chr2:171568250-171569199	HepG2	liver:	n/a	n/a
5	FOXA2	chr2:171568268-171569379	HepG2	liver:	n/a	chr2:171568937-171568949
6	FOXA1	chr2:171568222-171569101	HepG2	liver:	n/a	chr2:171568937-171568949
7	MAX	chr2:171567494-171574371	HepG2	liver:	n/a	chr2:171572484-171572494 chr2:171572090-171572100 chr2:171568528-171568538
8	CHD2	chr2:171568316-171569258	HepG2	liver:	n/a	chr2:171568521-171568531
9	PAX5	chr2:171569052-171569321	GM12878	blood:	n/a	n/a
10	NFIC	chr2:171568135-171569655	HepG2	liver:	n/a	n/a
11	HNF4G	chr2:171568280-171569478	HepG2	liver:	n/a	chr2:171568886-171568900 chr2:171568887-171568899 chr2:171568948-171568960 chr2:171568887-171568899 chr2:171568886-171568901 chr2:171568947-171568960
12	MBD4	chr2:171567758-171569279	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:171566521-171571156	HepG2	liver:	n/a	n/a
14	SIN3AK20	chr2:171568257-171569139	HepG2	liver:	n/a	n/a
15	POLR2A	chr2:171568156-171569522	HepG2	liver:	n/a	n/a
16	MAX	chr2:171567137-171574353	HepG2	liver:	n/a	chr2:171572484-171572494 chr2:171572090-171572100 chr2:171568528-171568538
17	TEAD4	chr2:171567582-171569561	HepG2	liver:	n/a	n/a
18	MYBL2	chr2:171566484-171570541	HepG2	liver:	n/a	n/a
19	HEY1	chr2:171566552-171576261	HepG2	liver:	n/a	chr2:171568717-171568732 chr2:171568723-171568738 chr2:171568409-171568424 chr2:171571862-171571877
20	NR2F2	chr2:171568175-171569165	HepG2	liver:	n/a	n/a
21	HNF4G	chr2:171568330-171569242	HepG2	liver:	n/a	chr2:171568886-171568900 chr2:171568887-171568899 chr2:171568948-171568960 chr2:171568887-171568899 chr2:171568886-171568901 chr2:171568947-171568960
22	HEY1	chr2:171566435-171575595	HepG2	liver:	n/a	chr2:171568717-171568732 chr2:171568723-171568738 chr2:171568409-171568424 chr2:171571862-171571877
23	EP300	chr2:171568307-171569146	HepG2	liver:	n/a	chr2:171568583-171568599 chr2:171568412-171568421 chr2:171568921-171568929 chr2:171568405-171568421
24	POLR2A	chr2:171567948-171571413	HepG2	liver:	n/a	n/a
25	TCF7L2	chr2:171568611-171569441	HEK293	kidney:	n/a	chr2:171568813-171568822 chr2:171568705-171568714 chr2:171568951-171568960 chr2:171568809-171568825
26	HNF4A	chr2:171568291-171569535	HepG2	liver:	n/a	chr2:171568886-171568900 chr2:171568887-171568899 chr2:171568948-171568960 chr2:171568887-171568899 chr2:171568947-171568960
27	POLR2A	chr2:171566818-171576833	HepG2	liver:	n/a	n/a
28	FOXA1	chr2:171568141-171569367	HepG2	liver:	n/a	chr2:171568937-171568949
29	CREB1	chr2:171567131-171573329	HepG2	liver:	n/a	n/a
30	POLR2A	chr2:171567743-171574223	HepG2	liver:	n/a	n/a
31	PAX5	chr2:171568948-171569307	GM12878	blood:	n/a	n/a
32	FOXA1	chr2:171568198-171569127	HepG2	liver:	n/a	chr2:171568937-171568949
33	PAX5	chr2:171568912-171569443	GM12878	blood:	n/a	n/a
34	TCF7L2	chr2:171568645-171569210	PANC-1	pancreas:	n/a	chr2:171568813-171568822 chr2:171568705-171568714 chr2:171568951-171568960 chr2:171568809-171568825
35	MAZ	chr2:171568336-171569417	HepG2	liver:	n/a	chr2:171568528-171568538
36	TBP	chr2:171567696-171569289	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:171566596-171571451	HepG2	liver:	n/a	n/a
38	RXRA	chr2:171568194-171569103	HepG2	liver:	n/a	chr2:171568885-171568901
39	SUZ12	chr2:171568999-171573118	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr2:171566701-171575246	HepG2	liver:	n/a	n/a
41	MBD4	chr2:171567491-171569843	HepG2	liver:	n/a	n/a
42	PAX5	chr2:171569019-171569248	GM12878	blood:	n/a	n/a
43	EP300	chr2:171568129-171569504	HepG2	liver:	n/a	chr2:171568583-171568599 chr2:171568412-171568421 chr2:171568921-171568929 chr2:171568405-171568421
44	HDAC2	chr2:171568182-171569403	HepG2	liver:	n/a	n/a
45	POLR2A	chr2:171567770-171569322	HepG2	liver:	n/a	n/a
46	HDAC2	chr2:171568274-171569122	HepG2	liver:	n/a	n/a
47	CTBP2	chr2:171567955-171571219	H1-hESC	embryonic stem cell:	n/a	n/a
48	MXI1	chr2:171567905-171569225	HepG2	liver:	n/a	n/a
49	YY1	chr2:171568567-171569378	HepG2	liver:	n/a	chr2:171568724-171568735 chr2:171568719-171568733 chr2:171568718-171568727
50	FOXA1	chr2:171568207-171569238	HepG2	liver:	n/a	chr2:171568937-171568949

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:171566974..171570291-chr2:171570602..171572475,4	MCF-7	breast:
2	chr2:171568787..171573894-chr2:171626202..171629385,10	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC007405.2.1-1	chr2:171568374-171570475	NONHSAT075415
2	lnc-AC007405.2.1-1	chr2:171568949-171571077	NR_027433

Variant related genes	Relation type
SP5	TF binding region
ENSG00000234350	Chromatin interaction
ENSG00000239467	Chromatin interaction
ENSG00000204335	Chromatin interaction
ENSG00000222033	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs16858900	1.00[AFR][1000 genomes]
rs16858920	1.00[AFR][1000 genomes]
rs17700577	1.00[AFR][1000 genomes]
rs17700773	1.00[AFR][1000 genomes]
rs17751683	1.00[AFR][1000 genomes]
rs1894918	1.00[AFR][1000 genomes]
rs2160414	1.00[AFR][1000 genomes]
rs45465192	1.00[AFR][1000 genomes]
rs45467694	1.00[AFR][1000 genomes]
rs45471500	1.00[AFR][1000 genomes]
rs45473292	1.00[AFR][1000 genomes]
rs45506192	1.00[AFR][1000 genomes]
rs4668310	1.00[AFR][1000 genomes]
rs4668311	1.00[AFR][1000 genomes]
rs4668322	1.00[AFR][1000 genomes]
rs4668328	1.00[AFR][1000 genomes]
rs4668330	1.00[AFR][1000 genomes]
rs701491	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875409	chr2:171565376-171577859	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv821786	chr2:171567780-171574707	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv583609	chr2:171568633-171573309	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv583610	chr2:171568633-171573529	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171560000-171570200	Weak transcription	Right Atrium	heart
2	chr2:171565200-171569800	Weak transcription	Gastric	stomach
3	chr2:171567800-171569200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:171567800-171569200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr2:171568000-171571600	Bivalent Enhancer	Fetal Brain Male	brain
6	chr2:171568200-171569200	Flanking Bivalent TSS/Enh	Thymus	Thymus
7	chr2:171568200-171569400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:171568200-171569800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr2:171568200-171569800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
10	chr2:171568200-171570600	Bivalent Enhancer	Fetal Stomach	stomach
11	chr2:171568400-171569600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
12	chr2:171568400-171570000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:171568400-171570200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
14	chr2:171568400-171570400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
15	chr2:171568400-171570400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
16	chr2:171568400-171570600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr2:171568400-171570600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr2:171568400-171571400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:171568600-171569200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:171568600-171569200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:171568600-171569800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
22	chr2:171568600-171570000	Enhancers	Pancreas	Pancrea
23	chr2:171568600-171570400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
24	chr2:171568600-171570600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
25	chr2:171568600-171570600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr2:171568800-171569200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:171568800-171569200	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:171568800-171569200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
29	chr2:171568800-171569200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
30	chr2:171568800-171569200	Bivalent Enhancer	Small Intestine	intestine
31	chr2:171568800-171569400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
32	chr2:171568800-171569600	Bivalent/Poised TSS	NHEK	skin
33	chr2:171568800-171569800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
34	chr2:171568800-171569800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
35	chr2:171568800-171570000	Bivalent Enhancer	Fetal Intestine Large	intestine
36	chr2:171568800-171570200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
37	chr2:171568800-171570200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:171568800-171570200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
39	chr2:171568800-171570200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:171568800-171570200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:171568800-171570200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:171568800-171570600	Bivalent Enhancer	Fetal Brain Female	brain
43	chr2:171568800-171570600	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr2:171568800-171570800	Bivalent Enhancer	Fetal Lung	lung
45	chr2:171569000-171569200	Flanking Bivalent TSS/Enh	ES-WA7 Cell Line	embryonic stem cell
46	chr2:171569000-171569200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
47	chr2:171569000-171569200	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr2:171569000-171569200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:171569000-171569200	Bivalent Enhancer	Liver	Liver
50	chr2:171569000-171569200	Bivalent Enhancer	Brain Germinal Matrix	brain

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