Variant report

Variant	rs2289236
Chromosome Location	chr2:127783406-127783407
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	JUND	chr2:127782333-127783570	H1-hESC	embryonic stem cell:	n/a	chr2:127782931-127782943 chr2:127782932-127782942 chr2:127782934-127782945 chr2:127782933-127782941
2	POLR2A	chr2:127783038-127783606	A549	lung:	n/a	n/a
3	CREB1	chr2:127783016-127783592	A549	lung:	n/a	n/a
4	CTCF	chr2:127782902-127783527	MCF-7	breast:	n/a	chr2:127783230-127783246 chr2:127783266-127783279
5	CTCF	chr2:127782916-127783438	A549	lung:	n/a	chr2:127783230-127783246 chr2:127783266-127783279
6	TBP	chr2:127782354-127783437	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr2:127782864-127783720	IMR90	lung:	n/a	chr2:127782999-127783011 chr2:127783266-127783280
8	RFX5	chr2:127783224-127783572	GM12878	blood:	n/a	n/a
9	YY1	chr2:127782199-127783533	H1-hESC	embryonic stem cell:	n/a	chr2:127783193-127783204 chr2:127782458-127782472 chr2:127783166-127783185
10	RUNX3	chr2:127783045-127783442	GM12878	blood:	n/a	n/a
11	HA-E2F1	chr2:127783060-127783688	MCF-7	breast:	n/a	chr2:127783562-127783569 chr2:127783562-127783569 chr2:127783562-127783569
12	MXI1	chr2:127783174-127783446	H1-hESC	embryonic stem cell:	n/a	n/a
13	JUND	chr2:127783100-127783571	A549	lung:	n/a	n/a
14	GATA3	chr2:127783236-127783876	SK-N-SH	brain:	n/a	n/a
15	MYC	chr2:127783295-127783520	K562	blood:	n/a	n/a
16	CTCF	chr2:127782074-127783952	SK-N-SH	brain:	n/a	chr2:127783230-127783246 chr2:127783266-127783279 chr2:127783537-127783550 chr2:127782458-127782471
17	CTCF	chr2:127783340-127783490	NHDF-neo	bronchial:	n/a	n/a
18	FOS	chr2:127783124-127783769	HUVEC	blood vessel:	n/a	n/a
19	CREB1	chr2:127782533-127783608	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZNF143	chr2:127782312-127783501	H1-hESC	embryonic stem cell:	n/a	chr2:127782434-127782453
21	MAX	chr2:127782186-127783539	H1-hESC	embryonic stem cell:	n/a	chr2:127782933-127782942 chr2:127782811-127782821 chr2:127783013-127783023
22	MXI1	chr2:127781934-127783919	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr2:127783014-127783597	A549	lung:	n/a	n/a
24	POLR2A	chr2:127782110-127783740	IMR90	lung:	n/a	n/a
25	POLR2A	chr2:127783010-127783711	H1-neurons	neurons:	n/a	n/a
26	GATA3	chr2:127783400-127783827	SH-SY5Y	brain:	n/a	n/a
27	MAX	chr2:127782782-127783700	A549	lung:	n/a	chr2:127782933-127782942 chr2:127782811-127782821 chr2:127783013-127783023
28	PBX3	chr2:127783061-127783730	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr2:127782983-127783690	U87	brain:	n/a	n/a
30	ZNF263	chr2:127782379-127783714	HEK293-T-REx	kidney:	n/a	n/a
31	POLR2A	chr2:127783093-127783475	A549	lung:	n/a	n/a
32	RAD21	chr2:127782947-127783482	A549	lung:	n/a	chr2:127782999-127783011 chr2:127783266-127783280
33	ELF1	chr2:127783039-127783655	MCF-7	breast:	n/a	n/a
34	RAD21	chr2:127782727-127783453	H1-hESC	embryonic stem cell:	n/a	chr2:127782999-127783011 chr2:127782817-127782826 chr2:127783266-127783280
35	BACH1	chr2:127783243-127783677	H1-hESC	embryonic stem cell:	n/a	n/a
36	NFYB	chr2:127783127-127783627	GM12878	blood:	n/a	chr2:127783441-127783451
37	POLR2A	chr2:127783081-127783470	A549	lung:	n/a	n/a
38	MAFK	chr2:127783168-127783704	IMR90	lung:	n/a	n/a
39	EP300	chr2:127783142-127783520	SK-N-SH_RA	brain:	n/a	chr2:127783228-127783244
40	TAF1	chr2:127783079-127783486	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr2:127783244-127783486	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr2:127782599-127783556	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr2:127782876-127783449	IMR90	lung:	n/a	chr2:127783230-127783246 chr2:127783266-127783279
44	REST	chr2:127782142-127783796	H1-neurons	neurons:	n/a	chr2:127783111-127783124 chr2:127782677-127782687 chr2:127783528-127783541
45	KAP1	chr2:127782247-127783728	U2OS	brain:	n/a	n/a
46	CTCF	chr2:127781993-127783826	A549	lung:	n/a	chr2:127783230-127783246 chr2:127783266-127783279 chr2:127783537-127783550 chr2:127782458-127782471
47	RAD21	chr2:127782779-127783523	A549	lung:	n/a	chr2:127782999-127783011 chr2:127782817-127782826 chr2:127783266-127783280
48	SIN3A	chr2:127782220-127783620	H1-hESC	embryonic stem cell:	n/a	chr2:127782367-127782377
49	E2F6	chr2:127782494-127783711	A549	lung:	n/a	chr2:127783562-127783569 chr2:127783562-127783569 chr2:127783562-127783569
50	MAZ	chr2:127783394-127783442	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:127783370-127783420	AG10803	skin:	n/a
2	chr2:127783370-127783420	HEEpiC	esophagus:	n/a
3	chr2:127783370-127783420	HepG2	liver:	n/a
4	chr2:127783370-127783420	AoSMC	blood vessel:	n/a
5	chr2:127783370-127783420	T-47D	breast:	n/a
6	chr2:127783370-127783420	Caco-2	colon:	n/a
7	chr2:127783370-127783420	SKMC	muscle:	n/a
8	chr2:127783370-127783420	GM06990	blood:	n/a
9	chr2:127783370-127783420	K562	blood:	n/a
10	chr2:127783370-127783420	GM12892	blood:	n/a
11	chr2:127783370-127783420	HRPEpiC	eye:	n/a
12	chr2:127783370-127783420	HCT-116	colon:	n/a
13	chr2:127783370-127783420	HPAEpiC	pulmonary alveolar:	n/a
14	chr2:127783370-127783420	SK-N-MC	brain:	n/a
15	chr2:127783370-127783420	Hela-S3	cervix:	n/a
16	chr2:127783370-127783420	ovcar-3	ovarian:	n/a
17	chr2:127783370-127783420	MCF-7	breast:	n/a
18	chr2:127783370-127783420	GM19239	blood:	n/a
19	chr2:127783370-127783420	Jurkat	blood:	n/a
20	chr2:127783370-127783420	HEK293	kidney:	embryo
21	chr2:127783370-127783420	HAEpiC	amniotic membrane:	n/a
22	chr2:127783370-127783420	GM12878	blood:	n/a
23	chr2:127783370-127783420	ProgFib	skin:	n/a
24	chr2:127783370-127783420	A549	lung:	n/a
25	chr2:127783370-127783420	RPTEC	kidney:	n/a
26	chr2:127783370-127783420	GM12891	blood:	n/a
27	chr2:127783370-127783420	AG04449	skin:	fetal
28	chr2:127783370-127783420	BE2_C	brain:	n/a
29	chr2:127783370-127783420	AG09319	gingival:	n/a
30	chr2:127783370-127783420	NHBE	bronchial:	n/a
31	chr2:127783370-127783420	NHDF-neo	bronchial:	n/a
32	chr2:127783370-127783420	Hepatocyte	liver:	n/a
33	chr2:127783370-127783420	HRCEpiC	kidney:	n/a
34	chr2:127783370-127783420	PFSK-1	brain:	n/a
35	chr2:127783370-127783420	U87	brain:	n/a
36	chr2:127783370-127783420	LNCaP	prostate:	n/a
37	chr2:127783370-127783420	IMR90	lung:	fetal
38	chr2:127783370-127783420	MCF10A-Er-Src	breast:	n/a
39	chr2:127783370-127783420	AG09309	skin:	n/a
40	chr2:127783370-127783420	PrEC	prostate:	n/a
41	chr2:127783370-127783420	NB4	blood:	n/a
42	chr2:127783370-127783420	HUVEC	blood vessel:	n/a
43	chr2:127783370-127783420	HMEC	breast:	n/a
44	chr2:127783370-127783420	NT2-D1	testis:	n/a
45	chr2:127783370-127783420	HRE	kidney:	n/a
46	chr2:127783370-127783420	NH-A	brain:	n/a
47	chr2:127783370-127783420	PANC-1	pancreas:	n/a
48	chr2:127783370-127783420	ECC-1	luminal epithelium:	n/a
49	chr2:127783370-127783420	AG04450	lung:	fetal
50	chr2:127783370-127783420	HCF	heart:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC114783.1.1-2	chr2:127782787-127787262	ENSG00000260163.1
2	lnc-AC114783.1.1-2	chr2:127782787-127783795	NONHSAT074140

Variant related genes	Relation type
ENSG00000260634	TF binding region
ENSG00000260634	CpG island

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1108031	0.94[EUR][1000 genomes]
rs3754618	0.93[EUR][1000 genomes]
rs3754620	0.93[EUR][1000 genomes]
rs60711884	0.94[EUR][1000 genomes]
rs6431218	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6720741	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6761879	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72843888	0.93[ASN][1000 genomes]
rs7557638	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7558000	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7558001	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7568161	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7594836	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7605172	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999422	chr2:127464647-127956543	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1004930	chr2:127477369-127938234	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	12 gene(s)	inside rSNPs	diseases
3	nsv834365	chr2:127616996-127793863	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv834366	chr2:127633714-127784692	Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv459230	chr2:127771006-127844735	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv583032	chr2:127771006-127844735	Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127782000-127783600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr2:127782200-127783600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr2:127782200-127783600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr2:127782200-127783600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:127782200-127783600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:127782200-127783600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:127782200-127783600	Active TSS	Brain Substantia Nigra	brain
8	chr2:127782200-127783800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr2:127782200-127783800	Active TSS	H1 Cell Line	embryonic stem cell
10	chr2:127782200-127783800	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr2:127782200-127784000	Active TSS	Brain Anterior Caudate	brain
12	chr2:127782200-127784000	Active TSS	Brain Germinal Matrix	brain
13	chr2:127782200-127784000	Active TSS	Fetal Brain Female	brain
14	chr2:127782200-127784000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr2:127782400-127783600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr2:127782400-127783600	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr2:127782400-127783600	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr2:127782400-127783600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:127782400-127783600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
20	chr2:127782400-127783600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
21	chr2:127782400-127783600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
22	chr2:127782400-127783600	Flanking Active TSS	Ovary	ovary
23	chr2:127782400-127783800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:127782400-127783800	Flanking Active TSS	NH-A	brain
25	chr2:127782400-127784000	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr2:127782400-127784000	Active TSS	A549	lung
27	chr2:127782600-127783600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr2:127782600-127783600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:127782600-127783600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
30	chr2:127782600-127783600	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr2:127782600-127783600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
32	chr2:127782600-127783600	Enhancers	Lung	lung
33	chr2:127782600-127783600	Flanking Active TSS	Pancreas	Pancrea
34	chr2:127782600-127783600	Flanking Active TSS	Right Ventricle	heart
35	chr2:127782600-127783600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
36	chr2:127782600-127783600	Flanking Active TSS	HMEC	breast
37	chr2:127782600-127783800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:127782600-127783800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:127782600-127783800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:127782600-127783800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:127782600-127783800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:127782600-127783800	Active TSS	Aorta	Aorta
43	chr2:127782600-127783800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:127782600-127783800	Flanking Active TSS	Fetal Lung	lung
45	chr2:127782600-127784000	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr2:127782800-127783600	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr2:127782800-127783600	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas
48	chr2:127782800-127783600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
49	chr2:127782800-127783600	Active TSS	Right Atrium	heart
50	chr2:127782800-127783600	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links