Variant report

Variant	rs13015236
Chromosome Location	chr2:190445936-190445937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:88)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:88 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:190444967-190446333	H1-neurons	neurons:	n/a	n/a
2	CEBPD	chr2:190445324-190445974	HepG2	liver:	n/a	n/a
3	TAL1	chr2:190445583-190447295	K562	blood:	n/a	chr2:190446828-190446846
4	HMGN3	chr2:190445150-190446945	K562	blood:	n/a	n/a
5	TCF12	chr2:190445408-190446118	ECC-1	luminal epithelium:	n/a	n/a
6	MAX	chr2:190445431-190446160	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr2:190445402-190446008	SK-N-SH	brain:	n/a	n/a
8	JUND	chr2:190445371-190446031	A549	lung:	n/a	chr2:190445807-190445816 chr2:190445760-190445774 chr2:190445854-190445863
9	MAZ	chr2:190445334-190446085	IMR90	lung:	n/a	n/a
10	HEY1	chr2:190444961-190446042	K562	blood:	n/a	chr2:190445659-190445674 chr2:190445648-190445663
11	SIN3AK20	chr2:190445491-190445958	K562	blood:	n/a	n/a
12	ELF1	chr2:190445527-190445964	K562	blood:	n/a	n/a
13	YY1	chr2:190445495-190446009	ECC-1	luminal epithelium:	n/a	chr2:190445850-190445864
14	MAX	chr2:190445533-190446022	SK-N-SH	brain:	n/a	n/a
15	TBP	chr2:190444906-190447343	K562	blood:	n/a	n/a
16	POLR2A	chr2:190445150-190445979	SK-N-MC	brain:	n/a	n/a
17	CTBP2	chr2:190444952-190446826	H1-hESC	embryonic stem cell:	n/a	n/a
18	HEY1	chr2:190445207-190446352	HepG2	liver:	n/a	chr2:190445659-190445674 chr2:190445648-190445663
19	PML	chr2:190444985-190445980	K562	blood:	n/a	n/a
20	MYC	chr2:190445034-190446078	K562	blood:	n/a	n/a
21	MBD4	chr2:190445539-190446352	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:190445377-190445977	A549	lung:	n/a	n/a
23	CCNT2	chr2:190445363-190446970	K562	blood:	n/a	chr2:190446828-190446848 chr2:190446371-190446380
24	MYBL2	chr2:190444837-190445936	HepG2	liver:	n/a	n/a
25	CREB1	chr2:190445019-190446109	K562	blood:	n/a	n/a
26	EP300	chr2:190445170-190446107	ECC-1	luminal epithelium:	n/a	chr2:190445946-190445955
27	POLR2A	chr2:190445099-190446029	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr2:190444982-190447214	K562	blood:	n/a	n/a
29	POLR2A	chr2:190444941-190446398	H1-neurons	neurons:	n/a	n/a
30	USF1	chr2:190445548-190446045	ECC-1	luminal epithelium:	n/a	n/a
31	YY1	chr2:190445168-190446411	HepG2	liver:	n/a	chr2:190445850-190445864 chr2:190446371-190446380
32	ZMIZ1	chr2:190445083-190447504	K562	blood:	n/a	n/a
33	MAX	chr2:190444884-190446055	A549	lung:	n/a	n/a
34	TAF1	chr2:190445339-190446185	H1-neurons	neurons:	n/a	n/a
35	KAP1	chr2:190445606-190445960	U2OS	brain:	n/a	n/a
36	MAX	chr2:190444851-190446159	A549	lung:	n/a	n/a
37	TCF12	chr2:190445436-190446172	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr2:190444897-190447250	K562	blood:	n/a	n/a
39	FOXA2	chr2:190445320-190445944	A549	lung:	n/a	n/a
40	POLR2A	chr2:190444227-190448816	PBDE	blood:	n/a	n/a
41	TAF1	chr2:190445325-190445962	A549	lung:	n/a	n/a
42	GATA1	chr2:190444265-190447639	PBDE	blood:	n/a	chr2:190446835-190446848 chr2:190444336-190444343 chr2:190446838-190446846 chr2:190444485-190444495 chr2:190446828-190446845
43	RCOR1	chr2:190444861-190447429	K562	blood:	n/a	n/a
44	POLR2A	chr2:190445009-190447207	K562	blood:	n/a	n/a
45	TCF12	chr2:190444963-190446236	A549	lung:	n/a	n/a
46	MAX	chr2:190445392-190445967	K562	blood:	n/a	n/a
47	MAX	chr2:190444898-190446430	HepG2	liver:	n/a	chr2:190446376-190446385 chr2:190446372-190446382
48	SP1	chr2:190445467-190446063	A549	lung:	n/a	n/a
49	POLR2A	chr2:190444989-190447536	K562	blood:	n/a	n/a
50	ARID3A	chr2:190445301-190446250	HepG2	liver:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:190445910-190445960	U87	brain:	n/a
2	chr2:190445910-190445960	GM12878	blood:	n/a
3	chr2:190445910-190445960	AG04449	skin:	fetal
4	chr2:190445910-190445960	SK-N-SH	brain:	n/a
5	chr2:190445910-190445960	Caco-2	colon:	n/a
6	chr2:190445910-190445960	HRPEpiC	eye:	n/a
7	chr2:190445910-190445960	GM19239	blood:	n/a
8	chr2:190445910-190445960	HL-60	blood:	n/a
9	chr2:190445910-190445960	HepG2	liver:	n/a
10	chr2:190445910-190445960	IMR90	lung:	fetal
11	chr2:190445910-190445960	HEEpiC	esophagus:	n/a
12	chr2:190445910-190445960	BJ	skin:	n/a
13	chr2:190445910-190445960	BE2_C	brain:	n/a
14	chr2:190445910-190445960	ovcar-3	ovarian:	n/a
15	chr2:190445910-190445960	GM12892	blood:	n/a
16	chr2:190445910-190445960	Jurkat	blood:	n/a
17	chr2:190445910-190445960	AoSMC	blood vessel:	n/a
18	chr2:190445910-190445960	ProgFib	skin:	n/a
19	chr2:190445910-190445960	CMK	blood:	n/a
20	chr2:190445910-190445960	AG10803	skin:	n/a
21	chr2:190445910-190445960	MCF-7	breast:	n/a
22	chr2:190445910-190445960	HIPEpiC	eye:	n/a
23	chr2:190445910-190445960	HUVEC	blood vessel:	n/a
24	chr2:190445910-190445960	AG09319	gingival:	n/a
25	chr2:190445910-190445960	Hela-S3	cervix:	n/a
26	chr2:190445910-190445960	NT2-D1	testis:	n/a
27	chr2:190445910-190445960	AG09309	skin:	n/a
28	chr2:190445910-190445960	HEK293	kidney:	embryo
29	chr2:190445910-190445960	HCPEpiC	choroid plexus:	n/a
30	chr2:190445910-190445960	HRCEpiC	kidney:	n/a
31	chr2:190445910-190445960	SK-N-MC	brain:	n/a
32	chr2:190445910-190445960	NB4	blood:	n/a
33	chr2:190445910-190445960	SK-N-SH_RA	brain:	n/a
34	chr2:190445910-190445960	NH-A	brain:	n/a
35	chr2:190445910-190445960	Hepatocyte	liver:	n/a
36	chr2:190445910-190445960	PrEC	prostate:	n/a
37	chr2:190445910-190445960	HAEpiC	amniotic membrane:	n/a
38	chr2:190445910-190445960	HCT-116	colon:	n/a
39	chr2:190445910-190445960	ECC-1	luminal epithelium:	n/a
40	chr2:190445910-190445960	LNCaP	prostate:	n/a
41	chr2:190445910-190445960	NHBE	bronchial:	n/a
42	chr2:190445910-190445960	HCF	heart:	n/a
43	chr2:190445910-190445960	SKMC	muscle:	n/a
44	chr2:190445910-190445960	HMEC	breast:	n/a
45	chr2:190445910-190445960	HCM	heart:	n/a
46	chr2:190445910-190445960	PANC-1	pancreas:	n/a
47	chr2:190445910-190445960	A549	lung:	n/a
48	chr2:190445910-190445960	MCF10A-Er-Src	breast:	n/a
49	chr2:190445910-190445960	GM12891	blood:	n/a
50	chr2:190445910-190445960	T-47D	breast:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190305660..190307734-chr2:190445889..190448100,2	K562	blood:
2	chr2:190443338..190447714-chr2:190524367..190527732,5	K562	blood:

No data

Variant related genes	Relation type
SLC40A1	TF binding region
SLC40A1	CpG island
ENSG00000115368	Chromatin interaction
ENSG00000138381	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1123110	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1439813	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1439814	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1439815	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4287798	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 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	chr2:190441600-190446400	Active TSS	Rectal Smooth Muscle	rectum
2	chr2:190441800-190446000	Active TSS	Stomach Smooth Muscle	stomach
3	chr2:190442200-190446400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:190442200-190446400	Active TSS	Aorta	Aorta
5	chr2:190442200-190446600	Active TSS	Right Atrium	heart
6	chr2:190443200-190446000	Active TSS	Fetal Muscle Leg	muscle
7	chr2:190443200-190446200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:190443200-190446200	Active TSS	Duodenum Mucosa	Duodenum
9	chr2:190443200-190446400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:190443200-190446600	Active TSS	Brain Anterior Caudate	brain
11	chr2:190443200-190446600	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr2:190443600-190446200	Active TSS	Fetal Intestine Large	intestine
13	chr2:190443600-190446400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:190443600-190446400	Active TSS	Ovary	ovary
15	chr2:190443800-190446000	Active TSS	Placenta	Placenta
16	chr2:190444000-190446400	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr2:190444000-190446600	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr2:190444200-190446200	Active TSS	Brain Angular Gyrus	brain
19	chr2:190444200-190446200	Active TSS	Fetal Stomach	stomach
20	chr2:190444200-190446600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr2:190444400-190446000	Active TSS	Liver	Liver
22	chr2:190444400-190446000	Active TSS	Fetal Brain Female	brain
23	chr2:190444400-190446200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr2:190444400-190446200	Active TSS	Colonic Mucosa	Colon
25	chr2:190444400-190446200	Active TSS	Fetal Muscle Trunk	muscle
26	chr2:190444400-190446200	Active TSS	Gastric	stomach
27	chr2:190444400-190446200	Active TSS	Left Ventricle	heart
28	chr2:190444400-190446200	Active TSS	Lung	lung
29	chr2:190444400-190446200	Active TSS	Pancreas	Pancrea
30	chr2:190444400-190446200	Active TSS	Right Ventricle	heart
31	chr2:190444400-190446200	Active TSS	Stomach Mucosa	stomach
32	chr2:190444400-190446400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
33	chr2:190444400-190446400	Active TSS	Brain Substantia Nigra	brain
34	chr2:190444400-190446600	Active TSS	Psoas Muscle	Psoas
35	chr2:190444400-190446800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr2:190444600-190446000	Active TSS	Monocytes-CD14+_RO01746	blood
37	chr2:190444600-190446200	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr2:190444600-190446200	Active TSS	Small Intestine	intestine
39	chr2:190444600-190446400	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr2:190444600-190446400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:190444600-190446400	Active TSS	Brain Inferior Temporal Lobe	brain
42	chr2:190444600-190446400	Active TSS	HSMMtube	muscle
43	chr2:190444800-190446000	Active TSS	Spleen	Spleen
44	chr2:190444800-190446200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:190444800-190446200	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr2:190444800-190446200	Active TSS	Esophagus	oesophagus
47	chr2:190444800-190446200	Active TSS	Fetal Lung	lung
48	chr2:190444800-190446400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr2:190444800-190446400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr2:190444800-190446400	Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links