Variant report

Variant	rs13390554
Chromosome Location	chr2:234196723-234196724
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF274	chr2:234196657-234196983	NT2-D1	testis:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:234196709-234196759	HCM	heart:	n/a
2	chr2:234196709-234196759	AG04449	skin:	fetal
3	chr2:234196709-234196759	U87	brain:	n/a
4	chr2:234196709-234196759	BE2_C	brain:	n/a
5	chr2:234196709-234196759	GM12892	blood:	n/a
6	chr2:234196709-234196759	HAEpiC	amniotic membrane:	n/a
7	chr2:234196709-234196759	GM12891	blood:	n/a
8	chr2:234196709-234196759	HCF	heart:	n/a
9	chr2:234196709-234196759	PrEC	prostate:	n/a
10	chr2:234196709-234196759	SKMC	muscle:	n/a
11	chr2:234196709-234196759	GM19239	blood:	n/a
12	chr2:234196709-234196759	NT2-D1	testis:	n/a
13	chr2:234196709-234196759	IMR90	lung:	fetal
14	chr2:234196709-234196759	NHBE	bronchial:	n/a
15	chr2:234196709-234196759	AG10803	skin:	n/a
16	chr2:234196709-234196759	HEK293	kidney:	embryo
17	chr2:234196709-234196759	SK-N-SH_RA	brain:	n/a
18	chr2:234196709-234196759	MCF-7	breast:	n/a
19	chr2:234196709-234196759	ECC-1	luminal epithelium:	n/a
20	chr2:234196709-234196759	HRPEpiC	eye:	n/a
21	chr2:234196709-234196759	AG04450	lung:	fetal
22	chr2:234196709-234196759	Hela-S3	cervix:	n/a
23	chr2:234196709-234196759	Caco-2	colon:	n/a
24	chr2:234196709-234196759	AG09319	gingival:	n/a
25	chr2:234196709-234196759	MCF10A-Er-Src	breast:	n/a
26	chr2:234196709-234196759	NH-A	brain:	n/a
27	chr2:234196709-234196759	HCT-116	colon:	n/a
28	chr2:234196709-234196759	AoSMC	blood vessel:	n/a
29	chr2:234196709-234196759	GM12878	blood:	n/a
30	chr2:234196709-234196759	HRCEpiC	kidney:	n/a
31	chr2:234196709-234196759	PFSK-1	brain:	n/a
32	chr2:234196709-234196759	PANC-1	pancreas:	n/a
33	chr2:234196709-234196759	NB4	blood:	n/a
34	chr2:234196709-234196759	AG09309	skin:	n/a
35	chr2:234196709-234196759	SK-N-MC	brain:	n/a
36	chr2:234196709-234196759	NHDF-neo	bronchial:	n/a
37	chr2:234196709-234196759	RPTEC	kidney:	n/a
38	chr2:234196709-234196759	HUVEC	blood vessel:	n/a
39	chr2:234196709-234196759	HMEC	breast:	n/a
40	chr2:234196709-234196759	HRE	kidney:	n/a
41	chr2:234196709-234196759	K562	blood:	n/a
42	chr2:234196709-234196759	HL-60	blood:	n/a
43	chr2:234196709-234196759	SK-N-SH	brain:	n/a
44	chr2:234196709-234196759	HPAEpiC	pulmonary alveolar:	n/a
45	chr2:234196709-234196759	ProgFib	skin:	n/a
46	chr2:234196709-234196759	HEEpiC	esophagus:	n/a
47	chr2:234196709-234196759	T-47D	breast:	n/a
48	chr2:234196709-234196759	A549	lung:	n/a
49	chr2:234196709-234196759	CMK	blood:	n/a
50	chr2:234196709-234196759	Hepatocyte	liver:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234184025..234186339-chr2:234195161..234196726,2	MCF-7	breast:
2	chr2:234160050..234162260-chr2:234194203..234196902,2	MCF-7	breast:
3	chr2:234159075..234160799-chr2:234195887..234199490,3	MCF-7	breast:

No data

Variant related genes	Relation type
SCARNA6	TF binding region
ATG16L1	TF binding region
ATG16L1	CpG island
SCARNA6	CpG island
ENSG00000085978	Chromatin interaction
ENSG00000252010	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13386783	0.83[AMR][1000 genomes]
rs13409759	0.83[AMR][1000 genomes]
rs13410746	0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs3792092	1.00[YRI][hapmap]
rs60212745	0.83[AMR][1000 genomes]
rs73110050	0.83[AMR][1000 genomes]
rs73112047	0.83[AMR][1000 genomes]
rs73114277	0.83[AMR][1000 genomes]
rs9973722	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][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	nsv584699	chr2:234182240-234255547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr2:234162200-234205200	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr2:234162200-234205200	Strong transcription	Fetal Muscle Trunk	muscle
3	chr2:234162400-234205200	Strong transcription	H1 Cell Line	embryonic stem cell
4	chr2:234162400-234205400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:234162600-234205000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:234162600-234205200	Strong transcription	Fetal Muscle Leg	muscle
7	chr2:234162800-234197000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:234162800-234205600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:234163200-234206000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:234164200-234205400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:234164200-234205400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:234164400-234196800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:234164400-234197200	Strong transcription	Adipose Nuclei	Adipose
14	chr2:234164600-234206000	Strong transcription	HepG2	liver
15	chr2:234165000-234206000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:234165200-234205400	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:234166800-234206000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:234169400-234197200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:234172200-234204800	Strong transcription	Placenta	Placenta
20	chr2:234176800-234207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:234177000-234206000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:234177200-234205400	Strong transcription	Dnd41	blood
23	chr2:234177800-234197200	Strong transcription	Left Ventricle	heart
24	chr2:234178400-234205200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:234179000-234206200	Strong transcription	Fetal Thymus	thymus
26	chr2:234179200-234205600	Strong transcription	Fetal Brain Female	brain
27	chr2:234179600-234204000	Strong transcription	HUVEC	blood vessel
28	chr2:234179600-234205400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:234179600-234205400	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:234179600-234205600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:234179800-234205200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr2:234180800-234206400	Strong transcription	Thymus	Thymus
33	chr2:234181000-234205200	Strong transcription	Liver	Liver
34	chr2:234181400-234216400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr2:234182400-234206000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:234183000-234204400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:234183200-234197400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:234184200-234197400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr2:234186800-234198200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:234187200-234198200	Weak transcription	Fetal Heart	heart
41	chr2:234187400-234198000	Weak transcription	Fetal Kidney	kidney
42	chr2:234189200-234205200	Strong transcription	Brain Germinal Matrix	brain
43	chr2:234189200-234205400	Strong transcription	Duodenum Mucosa	Duodenum
44	chr2:234189200-234205600	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr2:234189600-234205200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr2:234189800-234197400	Strong transcription	Lung	lung
47	chr2:234189800-234204600	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr2:234189800-234205200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:234190000-234197400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:234190000-234205000	Strong transcription	Aorta	Aorta

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