Variant report

Variant	rs6729043
Chromosome Location	chr2:115918857-115918858
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	SIN3A	chr2:115918518-115919187	H1-hESC	embryonic stem cell:	n/a	n/a
2	SP1	chr2:115918445-115919040	H1-hESC	embryonic stem cell:	n/a	chr2:115918982-115918994 chr2:115918984-115918993 chr2:115918983-115918993 chr2:115918979-115918993 chr2:115918984-115918993 chr2:115918982-115918994 chr2:115918983-115918993 chr2:115918983-115918992 chr2:115918833-115918844
3	RAD21	chr2:115918629-115919031	H1-hESC	embryonic stem cell:	n/a	chr2:115918976-115918990
4	RFX5	chr2:115918677-115919034	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUND	chr2:115918634-115919032	H1-hESC	embryonic stem cell:	n/a	chr2:115918982-115918991 chr2:115918954-115918968
6	GTF2F1	chr2:115918351-115918894	H1-hESC	embryonic stem cell:	n/a	n/a
7	JUND	chr2:115918652-115919066	H1-hESC	embryonic stem cell:	n/a	chr2:115918982-115918991 chr2:115919056-115919065 chr2:115918954-115918968
8	BACH1	chr2:115918502-115919163	H1-hESC	embryonic stem cell:	n/a	n/a
9	EGR1	chr2:115918552-115919037	H1-hESC	embryonic stem cell:	n/a	chr2:115918982-115918992
10	MAX	chr2:115918126-115919369	H1-hESC	embryonic stem cell:	n/a	chr2:115918279-115918290 chr2:115918281-115918288 chr2:115919292-115919302 chr2:115918279-115918289 chr2:115918278-115918286 chr2:115918280-115918289
11	CREB1	chr2:115918528-115919004	H1-hESC	embryonic stem cell:	n/a	n/a
12	SP1	chr2:115918457-115919172	H1-hESC	embryonic stem cell:	n/a	chr2:115918982-115918994 chr2:115918984-115918993 chr2:115918983-115918993 chr2:115918979-115918993 chr2:115918984-115918993 chr2:115918982-115918994 chr2:115918983-115918993 chr2:115919056-115919069 chr2:115918983-115918992 chr2:115918833-115918844
13	BHLHE40	chr2:115918816-115918957	HepG2	liver:	n/a	n/a
14	E2F6	chr2:115917958-115919412	H1-hESC	embryonic stem cell:	n/a	chr2:115918262-115918273 chr2:115919298-115919310 chr2:115918983-115918992 chr2:115918262-115918273 chr2:115919298-115919307 chr2:115919401-115919410
15	YY1	chr2:115918637-115919201	HepG2	liver:	n/a	chr2:115919088-115919102 chr2:115918983-115918992
16	TBP	chr2:115918793-115918992	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr2:115918095-115919702	H1-hESC	embryonic stem cell:	n/a	chr2:115918279-115918290 chr2:115918281-115918288 chr2:115919292-115919302 chr2:115918279-115918289 chr2:115918278-115918286 chr2:115918280-115918289
18	CTCF	chr2:115918780-115918930	WERI-Rb-1	eye:	n/a	n/a
19	JUND	chr2:115918778-115919073	H1-hESC	embryonic stem cell:	n/a	chr2:115918982-115918991 chr2:115919056-115919065 chr2:115918954-115918968
20	E2F6	chr2:115918091-115919655	H1-hESC	embryonic stem cell:	n/a	chr2:115918262-115918273 chr2:115919298-115919310 chr2:115918983-115918992 chr2:115918262-115918273 chr2:115919298-115919307 chr2:115919616-115919626 chr2:115919401-115919410

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC35F5-9	chr2:115918681-115918920	ENSG00000235026.1
2	lnc-SLC35F5-9	chr2:115918681-115918958	NONHSAT073869
3	lnc-SLC35F5-9	chr2:115918681-115918958	NONHSAT073871

Variant related genes	Relation type
DPP10-AS1	TF binding region
DPP10	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10182527	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10195710	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10445863	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10445864	0.83[ASN][1000 genomes]
rs10496484	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12613673	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12711818	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12711819	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12711821	0.84[ASN][1000 genomes]
rs17355498	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4356670	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4547539	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[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	nsv1014713	chr2:115858427-116018055	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3404972	chr2:115918007-115920855	Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv3387285	chr2:115918207-115920805	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:115918000-115919000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:115918000-115919800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:115918000-115920000	Active TSS	Brain Angular Gyrus	brain
4	chr2:115918000-115920000	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr2:115918000-115920600	Active TSS	Rectal Smooth Muscle	rectum
6	chr2:115918000-115920800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr2:115918000-115920800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr2:115918000-115921200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr2:115918200-115919800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:115918200-115919800	Active TSS	Colonic Mucosa	Colon
11	chr2:115918200-115920000	Active TSS	Fetal Brain Female	brain
12	chr2:115918200-115920200	Active TSS	Gastric	stomach
13	chr2:115918200-115920400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
14	chr2:115918200-115920400	Active TSS	Brain Anterior Caudate	brain
15	chr2:115918200-115920400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:115918200-115920800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr2:115918200-115921200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
18	chr2:115918400-115919000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:115918400-115919200	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr2:115918400-115919600	Bivalent/Poised TSS	Thymus	Thymus
21	chr2:115918400-115919800	Active TSS	Brain Substantia Nigra	brain
22	chr2:115918400-115920000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:115918400-115920000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:115918400-115920000	Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr2:115918400-115920200	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr2:115918400-115920600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:115918600-115919000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr2:115918600-115919000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
29	chr2:115918600-115919000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr2:115918600-115919000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:115918600-115919000	Bivalent/Poised TSS	Adipose Nuclei	Adipose
32	chr2:115918600-115919000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
33	chr2:115918600-115919200	Bivalent Enhancer	Primary B cells from cord blood	blood
34	chr2:115918600-115919200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:115918600-115919400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:115918600-115919400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
37	chr2:115918600-115919800	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:115918600-115919800	Active TSS	Fetal Intestine Large	intestine
39	chr2:115918600-115919800	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr2:115918600-115920000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:115918600-115920000	Active TSS	H9 Cell Line	embryonic stem cell
42	chr2:115918600-115920000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:115918600-115920000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:115918600-115920000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
45	chr2:115918600-115920000	Active TSS	Fetal Intestine Small	intestine
46	chr2:115918600-115920000	Active TSS	Fetal Kidney	kidney
47	chr2:115918600-115920200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:115918600-115920200	Active TSS	Brain Cingulate Gyrus	brain
49	chr2:115918600-115920600	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr2:115918600-115920800	Active TSS	Pancreatic Islets	Pancreatic Islet

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