Variant report

Variant	rs4744146
Chromosome Location	chr9:95569638-95569639
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr9:95569398-95572352	NT2-D1	testis:	n/a	n/a
2	PAX5	chr9:95569564-95569845	GM12892	blood:	n/a	chr9:95569633-95569651

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:95569618-95569668	AG04450	lung:	fetal
2	chr9:95569618-95569668	IMR90	lung:	fetal
3	chr9:95569618-95569668	ECC-1	luminal epithelium:	n/a
4	chr9:95569618-95569668	HNPCEpiC	eye:	n/a
5	chr9:95569618-95569668	Hela-S3	cervix:	n/a
6	chr9:95569618-95569668	BE2_C	brain:	n/a
7	chr9:95569618-95569668	HRE	kidney:	n/a
8	chr9:95569618-95569668	NH-A	brain:	n/a
9	chr9:95569618-95569668	NT2-D1	testis:	n/a
10	chr9:95569618-95569668	HCPEpiC	choroid plexus:	n/a
11	chr9:95569618-95569668	SKMC	muscle:	n/a
12	chr9:95569618-95569668	T-47D	breast:	n/a
13	chr9:95569618-95569668	GM12892	blood:	n/a
14	chr9:95569618-95569668	AG09319	gingival:	n/a
15	chr9:95569618-95569668	SK-N-MC	brain:	n/a
16	chr9:95569618-95569668	A549	lung:	n/a
17	chr9:95569618-95569668	HMEC	breast:	n/a
18	chr9:95569618-95569668	HepG2	liver:	n/a
19	chr9:95569618-95569668	HCT-116	colon:	n/a
20	chr9:95569618-95569668	HRPEpiC	eye:	n/a
21	chr9:95569618-95569668	PANC-1	pancreas:	n/a
22	chr9:95569618-95569668	HCF	heart:	n/a
23	chr9:95569618-95569668	LNCaP	prostate:	n/a
24	chr9:95569618-95569668	AG04449	skin:	fetal
25	chr9:95569618-95569668	GM12878	blood:	n/a
26	chr9:95569618-95569668	NHDF-neo	bronchial:	n/a
27	chr9:95569618-95569668	ovcar-3	ovarian:	n/a
28	chr9:95569618-95569668	K562	blood:	n/a
29	chr9:95569618-95569668	HPAEpiC	pulmonary alveolar:	n/a
30	chr9:95569618-95569668	GM12891	blood:	n/a
31	chr9:95569618-95569668	Caco-2	colon:	n/a
32	chr9:95569618-95569668	NHBE	bronchial:	n/a
33	chr9:95569618-95569668	AG09309	skin:	n/a
34	chr9:95569618-95569668	PFSK-1	brain:	n/a
35	chr9:95569618-95569668	NB4	blood:	n/a
36	chr9:95569618-95569668	HUVEC	blood vessel:	n/a
37	chr9:95569618-95569668	SK-N-SH	brain:	n/a
38	chr9:95569618-95569668	RPTEC	kidney:	n/a
39	chr9:95569618-95569668	Hepatocyte	liver:	n/a
40	chr9:95569618-95569668	AG10803	skin:	n/a
41	chr9:95569618-95569668	U87	brain:	n/a
42	chr9:95569618-95569668	HCM	heart:	n/a
43	chr9:95569618-95569668	GM19239	blood:	n/a
44	chr9:95569618-95569668	CMK	blood:	n/a
45	chr9:95569618-95569668	AoSMC	blood vessel:	n/a
46	chr9:95569618-95569668	SK-N-SH_RA	brain:	n/a
47	chr9:95569618-95569668	ProgFib	skin:	n/a
48	chr9:95569618-95569668	HEK293	kidney:	embryo
49	chr9:95569618-95569668	SAEC	small airway:	n/a
50	chr9:95569618-95569668	GM06990	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95431083..95433127-chr9:95569211..95571144,2	MCF-7	breast:
2	chr9:95563386..95565101-chr9:95567156..95569894,2	MCF-7	breast:

No data

Variant related genes	Relation type
ANKRD19P	TF binding region
ANKRD19P	CpG island
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10117449	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10118572	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10761171	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821018	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17380657	0.97[ASN][1000 genomes]
rs1812693	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011075	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35228290	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4744147	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv972420	chr9:95566045-95588965	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4744146	BICD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95569200-95571200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
2	chr9:95569400-95569800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
3	chr9:95569400-95569800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
4	chr9:95569400-95569800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:95569400-95569800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
6	chr9:95569400-95570000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr9:95569400-95570000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr9:95569400-95570000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr9:95569400-95570000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
10	chr9:95569400-95570000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:95569400-95570000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:95569400-95570000	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
13	chr9:95569400-95570000	Bivalent Enhancer	HMEC	breast
14	chr9:95569400-95570200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
15	chr9:95569400-95570200	Bivalent Enhancer	Fetal Heart	heart
16	chr9:95569400-95570600	Bivalent Enhancer	Primary B cells from cord blood	blood
17	chr9:95569400-95570600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:95569400-95571400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr9:95569400-95571600	Bivalent Enhancer	Fetal Muscle Leg	muscle
20	chr9:95569400-95572400	Bivalent Enhancer	Fetal Brain Male	brain
21	chr9:95569400-95572400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr9:95569400-95572400	Bivalent Enhancer	Fetal Thymus	thymus
23	chr9:95569600-95569800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
24	chr9:95569600-95569800	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
25	chr9:95569600-95569800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
26	chr9:95569600-95569800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:95569600-95569800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
28	chr9:95569600-95569800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:95569600-95569800	Bivalent/Poised TSS	Brain Angular Gyrus	brain
30	chr9:95569600-95569800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
31	chr9:95569600-95569800	Bivalent Enhancer	Brain Germinal Matrix	brain
32	chr9:95569600-95569800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
33	chr9:95569600-95569800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:95569600-95569800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
35	chr9:95569600-95569800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
36	chr9:95569600-95569800	Bivalent Enhancer	Rectal Smooth Muscle	rectum
37	chr9:95569600-95569800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
38	chr9:95569600-95569800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
39	chr9:95569600-95569800	Bivalent/Poised TSS	NHEK	skin
40	chr9:95569600-95570000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
41	chr9:95569600-95570000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
42	chr9:95569600-95570000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:95569600-95570000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
44	chr9:95569600-95570000	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
45	chr9:95569600-95570000	Bivalent Enhancer	Spleen	Spleen
46	chr9:95569600-95570200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:95569600-95570200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
48	chr9:95569600-95570200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
49	chr9:95569600-95570200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
50	chr9:95569600-95570200	Bivalent Enhancer	Left Ventricle	heart

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