Variant report

Variant	rs41269111
Chromosome Location	chr1:45960835-45960836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:45960198..45962227-chr1:46049813..46051584,2	K562	blood:
2	chr1:45810406..45813503-chr1:45959640..45961736,3	K562	blood:
3	chr1:45956531..45959150-chr1:45959417..45961826,2	MCF-7	breast:
4	chr1:45284333..45287601-chr1:45959122..45962141,3	K562	blood:
5	chr1:45954905..45960579-chr1:45960652..45966878,10	K562	blood:
6	chr1:45959289..45962571-chr1:45963704..45967328,6	MCF-7	breast:
7	chr1:45804184..45806968-chr1:45958652..45961269,2	K562	blood:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TESK2-1	chr1:45959609-45960838	NONHSAT002941
2	lnc-TESK2-1	chr1:45960148-45960838	NONHSAT002942
3	lnc-TESK2-1	chr1:45959598-45960838	NR_033298
4	lnc-TESK2-1	chr1:45959598-45960838	NR_033297
5	lnc-TESK2-1	chr1:45959598-45960838	NR_033296

No data

Variant related genes	Relation type
ENSG00000070759	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000132781	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12073132	1.00[ASN][1000 genomes]
rs2275084	1.00[EUR][1000 genomes]
rs2297652	1.00[EUR][1000 genomes]
rs28365868	1.00[EUR][1000 genomes]
rs28365913	1.00[EUR][1000 genomes]
rs3748645	1.00[EUR][1000 genomes]
rs3811433	1.00[EUR][1000 genomes]
rs3811434	1.00[EUR][1000 genomes]
rs41269109	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269115	1.00[EUR][1000 genomes]
rs41272133	1.00[EUR][1000 genomes]
rs41312018	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56215132	1.00[EUR][1000 genomes]
rs56220330	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45956800-45964600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:45956800-45964800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:45956800-45964800	Weak transcription	Spleen	Spleen
4	chr1:45956800-45965000	Weak transcription	Gastric	stomach
5	chr1:45956800-45974000	Weak transcription	Small Intestine	intestine
6	chr1:45957000-45962600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:45957000-45964200	Weak transcription	Pancreas	Pancrea
8	chr1:45957000-45964400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:45957000-45964600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:45957000-45964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:45957200-45961800	Weak transcription	Lung	lung
12	chr1:45957200-45964200	Weak transcription	K562	blood
13	chr1:45957400-45964000	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:45957400-45964600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:45957400-45965200	Weak transcription	HSMM	muscle
16	chr1:45957600-45961800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:45957600-45962200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:45957600-45964000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:45957600-45964000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:45957600-45964200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:45957600-45964200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:45957600-45964200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:45957600-45964400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:45957600-45964600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:45957600-45964600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:45957600-45964600	Weak transcription	Ovary	ovary
27	chr1:45957600-45964600	Weak transcription	Thymus	Thymus
28	chr1:45957600-45964600	Weak transcription	Osteobl	bone
29	chr1:45957600-45964800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:45957600-45964800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:45957600-45964800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:45957600-45965000	Weak transcription	Psoas Muscle	Psoas
33	chr1:45957800-45961800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:45957800-45961800	Weak transcription	Esophagus	oesophagus
35	chr1:45957800-45961800	Weak transcription	Left Ventricle	heart
36	chr1:45957800-45961800	Weak transcription	Right Atrium	heart
37	chr1:45957800-45961800	Weak transcription	NHEK	skin
38	chr1:45957800-45962000	Weak transcription	Placenta	Placenta
39	chr1:45957800-45962200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:45957800-45962200	Weak transcription	Fetal Stomach	stomach
41	chr1:45957800-45964000	Weak transcription	Liver	Liver
42	chr1:45957800-45964000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:45957800-45964000	Weak transcription	Brain Substantia Nigra	brain
44	chr1:45957800-45964200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:45957800-45964400	Weak transcription	Brain Angular Gyrus	brain
46	chr1:45957800-45964400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:45957800-45964600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:45957800-45964600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:45957800-45964800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:45957800-45964800	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links