Variant report

Variant	rs41309078
Chromosome Location	chr2:231081885-231081886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:231072082..231074333-chr2:231080031..231082815,2	MCF-7	breast:
2	chr2:231080762..231082857-chr2:231083207..231085642,2	K562	blood:
3	chr2:231081815..231083756-chr2:231088866..231091364,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135899	Chromatin interaction
ENSG00000079263	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1010491	0.88[ASN][1000 genomes]
rs10205568	0.90[ASN][1000 genomes]
rs16826932	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1946409	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35253977	0.90[ASN][1000 genomes]
rs35540610	0.92[ASN][1000 genomes]
rs55657711	0.90[ASN][1000 genomes]
rs55796826	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55947860	0.90[ASN][1000 genomes]
rs56083766	0.90[ASN][1000 genomes]
rs56246923	0.95[ASN][1000 genomes]
rs57841972	0.90[ASN][1000 genomes]
rs6436923	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6436924	0.97[ASN][1000 genomes]
rs66596912	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs66673816	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs67138220	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs67994404	0.92[ASN][1000 genomes]
rs72986394	0.93[ASN][1000 genomes]
rs72988209	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72988279	0.93[ASN][1000 genomes]
rs72990219	0.88[ASN][1000 genomes]
rs72990227	0.81[ASN][1000 genomes]
rs73104283	0.90[ASN][1000 genomes]
rs7580269	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584666	chr2:231050715-231106621	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231059000-231082800	Weak transcription	Stomach Mucosa	stomach
2	chr2:231062600-231082200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:231062600-231082400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:231062600-231084200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr2:231063000-231084000	Weak transcription	Hela-S3	cervix
6	chr2:231063200-231084000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:231063400-231082200	Strong transcription	Fetal Muscle Leg	muscle
8	chr2:231064800-231084000	Weak transcription	Fetal Heart	heart
9	chr2:231066200-231083200	Weak transcription	HUVEC	blood vessel
10	chr2:231066200-231084400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:231067600-231084200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:231068200-231082200	Strong transcription	Ovary	ovary
13	chr2:231068200-231084400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:231068400-231084000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:231071800-231084200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:231073600-231084000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:231074200-231084000	Weak transcription	Fetal Kidney	kidney
18	chr2:231075400-231082000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr2:231076000-231084200	Weak transcription	Brain Angular Gyrus	brain
20	chr2:231076800-231084000	Weak transcription	NHDF-Ad	bronchial
21	chr2:231077400-231084000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:231077400-231084000	Weak transcription	NH-A	brain
23	chr2:231077400-231084000	Weak transcription	Osteobl	bone
24	chr2:231077400-231084200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:231077600-231084000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:231077800-231082800	Weak transcription	HepG2	liver
27	chr2:231077800-231084000	Weak transcription	NHLF	lung
28	chr2:231078000-231082000	Weak transcription	Fetal Intestine Small	intestine
29	chr2:231078000-231082600	Weak transcription	Colonic Mucosa	Colon
30	chr2:231078000-231082600	Weak transcription	Psoas Muscle	Psoas
31	chr2:231078000-231084200	Weak transcription	Pancreas	Pancrea
32	chr2:231078400-231082000	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr2:231078800-231082600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:231079000-231082400	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:231079000-231084000	Weak transcription	Brain Anterior Caudate	brain
36	chr2:231079200-231082400	Weak transcription	Brain Substantia Nigra	brain
37	chr2:231079200-231083200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr2:231079200-231083800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:231079200-231084200	Weak transcription	Esophagus	oesophagus
40	chr2:231079600-231082400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr2:231079800-231083200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:231079800-231084200	Weak transcription	Gastric	stomach
43	chr2:231080000-231082200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
44	chr2:231080200-231082400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr2:231080200-231082600	Genic enhancers	Primary T cells fromperipheralblood	blood
46	chr2:231080600-231082000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr2:231080600-231082600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr2:231080600-231082600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:231080600-231082800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:231080600-231083000	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links