Variant report

Variant	rs935376
Chromosome Location	chr2:47039991-47039992
allele	C/T
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	GATA3	chr2:47039121-47040635	SK-N-SH	brain:	n/a	n/a
2	TAF1	chr2:47039323-47040040	SK-N-SH	brain:	n/a	n/a
3	CEBPB	chr2:47039771-47040074	A549	lung:	n/a	chr2:47039930-47039941
4	POLR2A	chr2:47038886-47040804	SK-N-SH	brain:	n/a	n/a
5	PBX3	chr2:47039138-47040781	SK-N-SH	brain:	n/a	n/a
6	CEBPB	chr2:47039691-47040179	A549	lung:	n/a	chr2:47039930-47039941
7	NFIC	chr2:47038968-47040824	SK-N-SH	brain:	n/a	n/a
8	TEAD4	chr2:47039144-47040410	SK-N-SH	brain:	n/a	n/a
9	RCOR1	chr2:47039736-47039998	K562	blood:	n/a	n/a
10	POLR2A	chr2:47039729-47040004	ProgFib	skin:	n/a	n/a
11	CEBPB	chr2:47039832-47040065	K562	blood:	n/a	chr2:47039930-47039941
12	PBX3	chr2:47039215-47040687	SK-N-SH	brain:	n/a	n/a
13	NFIC	chr2:47039134-47040716	SK-N-SH	brain:	n/a	n/a
14	EP300	chr2:47039184-47040749	SK-N-SH_RA	brain:	n/a	chr2:47039929-47039943
15	YY1	chr2:47039640-47040191	SK-N-SH_RA	brain:	n/a	n/a
16	EP300	chr2:47039047-47040563	SK-N-SH_RA	brain:	n/a	chr2:47039929-47039943
17	MAX	chr2:47039324-47040566	SK-N-SH	brain:	n/a	n/a
18	SP1	chr2:47039196-47040179	A549	lung:	n/a	chr2:47039294-47039301
19	TCF12	chr2:47039076-47040890	SK-N-SH	brain:	n/a	chr2:47039504-47039512 chr2:47039262-47039270
20	SP1	chr2:47039516-47040168	A549	lung:	n/a	n/a
21	RAD21	chr2:47039259-47040516	SK-N-SH_RA	brain:	n/a	chr2:47039275-47039284 chr2:47039328-47039338
22	MAX	chr2:47039366-47040639	SK-N-SH	brain:	n/a	n/a
23	TCF12	chr2:47039101-47040929	SK-N-SH	brain:	n/a	chr2:47039504-47039512 chr2:47039262-47039270
24	RXRA	chr2:47038999-47040683	SK-N-SH	brain:	n/a	chr2:47039439-47039455
25	MAFK	chr2:47039643-47040087	IMR90	lung:	n/a	n/a
26	REST	chr2:47039352-47040471	SK-N-SH	brain:	n/a	chr2:47040085-47040098 chr2:47040123-47040136
27	RXRA	chr2:47039178-47040202	SK-N-SH	brain:	n/a	chr2:47039439-47039455
28	RAD21	chr2:47039592-47039991	IMR90	lung:	n/a	n/a
29	CEBPB	chr2:47039684-47040126	IMR90	lung:	n/a	chr2:47039930-47039941
30	TCF12	chr2:47039449-47040192	A549	lung:	n/a	chr2:47039504-47039512
31	CEBPB	chr2:47039857-47040040	Hela-S3	cervix:	n/a	chr2:47039930-47039941
32	SIN3AK20	chr2:47039749-47040027	SK-N-SH	brain:	n/a	n/a
33	CEBPB	chr2:47039633-47040189	A549	lung:	n/a	chr2:47039930-47039941
34	ZNF263	chr2:47039620-47040526	HEK293-T-REx	kidney:	n/a	chr2:47040114-47040135
35	TEAD4	chr2:47039118-47040521	SK-N-SH	brain:	n/a	n/a
36	EP300	chr2:47037776-47041932	SK-N-SH	brain:	n/a	chr2:47041533-47041547 chr2:47038862-47038876 chr2:47039929-47039943
37	YY1	chr2:47039607-47040502	SK-N-SH_RA	brain:	n/a	n/a
38	POLR2A	chr2:47039304-47040491	SK-N-SH	brain:	n/a	n/a
39	REST	chr2:47039404-47040023	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr2:47039556-47040073	IMR90	lung:	n/a	n/a
41	SIN3AK20	chr2:47039380-47040476	SK-N-SH	brain:	n/a	n/a
42	GATA3	chr2:47039113-47040781	SK-N-SH	brain:	n/a	n/a
43	RAD21	chr2:47039241-47040627	SK-N-SH_RA	brain:	n/a	chr2:47039275-47039284 chr2:47039328-47039338
44	EP300	chr2:47039029-47040807	SK-N-SH	brain:	n/a	chr2:47039929-47039943
45	EP300	chr2:47039069-47040473	SK-N-SH	brain:	n/a	chr2:47039929-47039943

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47038370..47041063-chr2:47049130..47051492,2	K562	blood:

Variant related genes	Relation type
LINC01119	TF binding region
LINC01118	TF binding region

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

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs4953424	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs935375	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 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	chr2:47031400-47043600	Weak transcription	Spleen	Spleen
2	chr2:47031400-47052000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:47037600-47042400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:47038000-47042600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:47038200-47042400	Enhancers	Fetal Stomach	stomach
6	chr2:47038200-47042600	Enhancers	NHDF-Ad	bronchial
7	chr2:47038200-47042800	Enhancers	Colon Smooth Muscle	Colon
8	chr2:47038400-47040600	Enhancers	Duodenum Smooth Muscle	Duodenum
9	chr2:47038400-47041400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:47038400-47041600	Enhancers	Fetal Lung	lung
11	chr2:47038600-47042000	Enhancers	Brain Anterior Caudate	brain
12	chr2:47038600-47042000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:47038600-47042400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:47038600-47042400	Enhancers	Fetal Muscle Leg	muscle
15	chr2:47038600-47042400	Enhancers	Ovary	ovary
16	chr2:47038600-47042400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr2:47038600-47042600	Enhancers	Rectal Smooth Muscle	rectum
18	chr2:47038600-47042600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr2:47038600-47042800	Enhancers	Left Ventricle	heart
20	chr2:47038600-47046400	Enhancers	Lung	lung
21	chr2:47038600-47046400	Enhancers	Right Atrium	heart
22	chr2:47038800-47040200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr2:47038800-47041800	Enhancers	Fetal Muscle Trunk	muscle
24	chr2:47038800-47042800	Enhancers	Fetal Heart	heart
25	chr2:47038800-47043800	Enhancers	Placenta	Placenta
26	chr2:47038800-47044000	Weak transcription	Esophagus	oesophagus
27	chr2:47038800-47046200	Enhancers	Right Ventricle	heart
28	chr2:47039000-47040400	Enhancers	Brain Germinal Matrix	brain
29	chr2:47039200-47040000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:47039200-47040200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:47039200-47040200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:47039200-47040200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:47039200-47040200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:47039200-47040200	Enhancers	Fetal Intestine Small	intestine
35	chr2:47039200-47040400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr2:47039200-47040600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr2:47039200-47040600	Enhancers	Duodenum Mucosa	Duodenum
38	chr2:47039200-47042000	Enhancers	Colonic Mucosa	Colon
39	chr2:47039200-47042200	Enhancers	Adipose Nuclei	Adipose
40	chr2:47039400-47040000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:47039400-47040000	Weak transcription	Fetal Thymus	thymus
42	chr2:47039400-47040000	Flanking Active TSS	NH-A	brain
43	chr2:47039400-47040200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:47039400-47040200	Enhancers	NHEK	skin
45	chr2:47039400-47040400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr2:47039400-47040400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:47039400-47040600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:47039400-47040600	Enhancers	Brain Angular Gyrus	brain
49	chr2:47039400-47040600	Enhancers	Fetal Brain Male	brain
50	chr2:47039400-47040600	Flanking Active TSS	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links