Variant report

Variant	rs60661938
Chromosome Location	chr2:85841520-85841521
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
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	POLR2A	chr2:85841330-85841593	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85643378..85649324-chr2:85837656..85846268,13	K562	blood:
2	chr2:85765143..85767907-chr2:85841259..85844982,5	MCF-7	breast:
3	chr2:85555692..85557938-chr2:85839320..85841664,2	K562	blood:
4	chr2:85786982..85789648-chr2:85837896..85843296,4	MCF-7	breast:
5	chr2:85545715..85547483-chr2:85839684..85842184,2	K562	blood:
6	chr2:85764765..85769369-chr2:85840508..85847982,10	K562	blood:
7	chr2:85837207..85840832-chr2:85841070..85844212,15	K562	blood:

No data

Variant related genes	Relation type
USP39	TF binding region
C2orf68	TF binding region
ENSG00000118640	Chromatin interaction
ENSG00000168887	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000042493	Chromatin interaction
ENSG00000168883	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000115486	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs3024803	0.87[AMR][1000 genomes]
rs3024805	0.87[AMR][1000 genomes]
rs3024810	0.87[AMR][1000 genomes]
rs3024811	0.87[AMR][1000 genomes]
rs3024815	1.00[AMR][1000 genomes]
rs3024818	1.00[AMR][1000 genomes]
rs3024819	1.00[AMR][1000 genomes]
rs3024822	1.00[AMR][1000 genomes]
rs3024827	1.00[AMR][1000 genomes]
rs3024828	1.00[AMR][1000 genomes]
rs4416212	0.89[AFR][1000 genomes]
rs57175088	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57762218	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57789237	0.87[AMR][1000 genomes]
rs59048598	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59139634	0.88[AFR][1000 genomes]
rs59227664	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60755293	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60801683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61535370	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61536745	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6547627	1.00[ASN][1000 genomes]
rs6718028	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923039	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72923051	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923062	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923064	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923077	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923080	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923082	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7564769	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7579847	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7580358	0.87[AMR][1000 genomes]
rs7584055	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7589436	0.87[AMR][1000 genomes]
rs7599812	0.98[AFR][1000 genomes];1.00[AMR][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	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85839600-85842400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:85839600-85842600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr2:85839600-85842600	Weak transcription	Brain Angular Gyrus	brain
4	chr2:85839600-85842600	Weak transcription	Fetal Heart	heart
5	chr2:85839600-85842800	Weak transcription	Esophagus	oesophagus
6	chr2:85839600-85843000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr2:85839600-85843200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:85839800-85842400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:85839800-85842400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:85839800-85842400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:85839800-85842400	Weak transcription	Adipose Nuclei	Adipose
12	chr2:85839800-85842400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:85839800-85842400	Weak transcription	GM12878-XiMat	blood
14	chr2:85839800-85842600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:85839800-85842600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:85839800-85842600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:85839800-85842600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:85839800-85842600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:85839800-85842600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr2:85839800-85842600	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr2:85839800-85842600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:85839800-85842600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr2:85839800-85842600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:85839800-85842600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr2:85839800-85842600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:85839800-85842600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:85839800-85842600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:85839800-85842600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:85839800-85842600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:85839800-85842600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:85839800-85842600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:85839800-85842600	Weak transcription	Liver	Liver
33	chr2:85839800-85842600	Weak transcription	Brain Anterior Caudate	brain
34	chr2:85839800-85842600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:85839800-85842600	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:85839800-85842600	Weak transcription	Fetal Intestine Large	intestine
37	chr2:85839800-85842600	Weak transcription	Fetal Lung	lung
38	chr2:85839800-85842600	Weak transcription	Fetal Thymus	thymus
39	chr2:85839800-85842600	Weak transcription	Pancreas	Pancrea
40	chr2:85839800-85842600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:85839800-85842600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:85839800-85842600	Weak transcription	Stomach Mucosa	stomach
43	chr2:85839800-85842600	Weak transcription	Spleen	Spleen
44	chr2:85839800-85842600	Weak transcription	A549	lung
45	chr2:85839800-85842600	Weak transcription	NH-A	brain
46	chr2:85839800-85842600	Weak transcription	Osteobl	bone
47	chr2:85839800-85842800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:85839800-85842800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:85839800-85842800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr2:85839800-85842800	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links