Variant report

Variant	rs1860699
Chromosome Location	chr2:235127466-235127467
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	RAD21	chr2:235127184-235127565	SK-N-SH_RA	brain:	n/a	n/a
2	TCF12	chr2:235126714-235127744	SK-N-SH	brain:	n/a	n/a
3	EP300	chr2:235127203-235127553	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000261298	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1013546	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10178233	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1029890	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12617671	0.81[EUR][1000 genomes]
rs7421360	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv584713	chr2:235092011-235236611	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:235123400-235128800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr2:235123600-235128200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:235123600-235128200	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr2:235123800-235128200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:235124000-235128000	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr2:235124000-235128400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:235124400-235128800	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr2:235124600-235127600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:235124600-235129000	Enhancers	Dnd41	blood
10	chr2:235124800-235127600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr2:235124800-235128000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:235124800-235128000	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr2:235125600-235127600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr2:235125600-235127600	Enhancers	NHEK	skin
15	chr2:235125800-235127600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:235125800-235127800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:235125800-235128400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:235125800-235128400	Enhancers	Primary T cells from cord blood	blood
19	chr2:235126800-235127600	Enhancers	Adipose Nuclei	Adipose
20	chr2:235126800-235127600	Enhancers	Fetal Muscle Leg	muscle
21	chr2:235126800-235127600	Enhancers	Fetal Thymus	thymus
22	chr2:235126800-235128000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:235126800-235128600	Enhancers	Brain Germinal Matrix	brain
24	chr2:235127000-235127600	Enhancers	Small Intestine	intestine
25	chr2:235127000-235127800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:235127000-235127800	Enhancers	Duodenum Mucosa	Duodenum
27	chr2:235127000-235127800	Enhancers	Fetal Kidney	kidney
28	chr2:235127000-235128000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:235127000-235128200	Enhancers	Thymus	Thymus
30	chr2:235127000-235128200	Enhancers	NHDF-Ad	bronchial
31	chr2:235127000-235128400	Enhancers	Fetal Brain Female	brain
32	chr2:235127000-235128600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr2:235127200-235127600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:235127200-235127600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:235127200-235127600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:235127200-235127600	Enhancers	NHLF	lung
37	chr2:235127200-235127800	Enhancers	Fetal Intestine Small	intestine
38	chr2:235127200-235127800	Enhancers	Fetal Lung	lung
39	chr2:235127200-235127800	Enhancers	A549	lung
40	chr2:235127200-235128400	Enhancers	Fetal Brain Male	brain
41	chr2:235127200-235130000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:235127400-235127600	Enhancers	Duodenum Smooth Muscle	Duodenum

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