Variant report

Variant	rs6587948
Chromosome Location	chr1:62331575-62331576
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11207848	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs1286813	0.82[JPT][hapmap]
rs1572670	0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2788615	0.86[ASN][1000 genomes]
rs2799625	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2811325	0.83[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs4456122	0.89[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000294	chr1:61746280-62350718	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
2	esv3693319	chr1:62207254-62402549	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv830004	chr1:62242944-62382228	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62228600-62391800	Weak transcription	Small Intestine	intestine
2	chr1:62263800-62343600	Weak transcription	Colonic Mucosa	Colon
3	chr1:62264600-62335600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:62285600-62338000	Weak transcription	Fetal Kidney	kidney
5	chr1:62293800-62343200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:62308800-62331600	Weak transcription	Stomach Mucosa	stomach
7	chr1:62312800-62353200	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:62313200-62339400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:62316200-62352200	Weak transcription	Brain Anterior Caudate	brain
10	chr1:62317800-62390400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:62319000-62373800	Weak transcription	Brain Angular Gyrus	brain
12	chr1:62320000-62334200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:62320200-62335400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:62320200-62349800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:62320400-62335200	Weak transcription	Brain Germinal Matrix	brain
16	chr1:62320800-62331800	Strong transcription	Fetal Intestine Small	intestine
17	chr1:62320800-62334400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:62320800-62334600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:62320800-62353200	Weak transcription	A549	lung
20	chr1:62321000-62332000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:62321000-62343600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:62321200-62331800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:62321400-62333200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:62321400-62334200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:62321600-62333800	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:62321600-62353200	Weak transcription	Adipose Nuclei	Adipose
27	chr1:62322000-62335000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:62322400-62332400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:62323600-62331800	Strong transcription	Fetal Intestine Large	intestine
30	chr1:62323600-62335200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr1:62323600-62335400	Weak transcription	Fetal Brain Female	brain
32	chr1:62323800-62355200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr1:62324400-62361000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:62324600-62336000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:62325000-62357400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:62326000-62331800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr1:62327400-62331800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:62327400-62332000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:62327800-62337800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr1:62328400-62335400	Weak transcription	Spleen	Spleen
41	chr1:62329000-62331800	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr1:62329000-62331800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr1:62329000-62333000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:62329000-62333400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:62329400-62331800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr1:62329400-62331800	Strong transcription	Liver	Liver
47	chr1:62329400-62332000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:62329400-62332000	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr1:62329600-62331800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr1:62329600-62331800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links